That’s what @BostonJeremy77 already mentioned a day ago in his second reply. 
Here’s a wishlist topic, please vote
I saw that . He made a great point but as he said “controller” I only focused on the joystick and the joystick button bindings. I should have also looked at keyboard bindings my mistake! Anyway I’m grateful for all replies. Problem solved
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Thank you! I fly with the joystick and use the keyboard numpad just for cockpit cam hotkey views 
However you make a very good point: in essence the game was accepting 2 inputs + autopilot. The stick which controls pitch/yaw/roll & the (inadvertent) numpad keys which also were controlling pitch/yaw/roll.
So when I pressed a view key it was also deflecting a control surface! All deleted now. I hope your wish will be granted by Asobo team. If a controller is plugged in the game should pop up a notice:
Controller detected. Disable keyboard primary flight controls?
[Yes] ______ [No]
Just a point of detail.
Your controller is not disabled when AP is engaged. Just like the real thing, it requires a determined effort from the pilot, (in most cases) to override the AP. If the control input reaches a defined limit the AP disengages. Any input in the sim results in the AP fighting against it until it disengages.
This is why there is a warning from the system when the AP disengages. There was a total loss flight that involved an inadvertent 'knee press" against the control column while dealing with a burned out landing gear indicator light. The warning was not sufficient to alert the flight crew, resulting in a loss of altitude and CFIT. (Controlled Flight Into Ground)
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Happy you found a solution. Can I ask why there was a need for this comment “Absolutely ridiculous that this game has not sorted out this most basic feature that FS2004, FSX, P3D, X-Plane 11 have working so well. I threw a lot of money at the Premium Deluxe. I expect these things to just work!”. I just sigh when users default to comments like these. Doesnt really help anyone.
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Alas, the sim does not implement that “effort evaluation”, at least not for keyboard. An AP disengage does not happen in MSFS unless you press “Z” or the little red button. I’m sure of this. I tried quite some effort. Not being aware of any AP being active, I struggled over an hour with this silly AP and it (or we) crashed my Cessna 4x. I tried a lot of extreme effort but the AP kept resisting. rigorously. Isn’t there some safety bounds ? On keyboard, when I steer against the AP, I see the autopilot sustain aileron, until it initiates a spin. Could this happen in a real 172 ? I would imagine they’d build some kind of maximum excursion angle for aeleron and elevator AP ? When would an AP need to do an extreme correction…
I wonder if this issue could be a bug in the keyboard input when AP is on. What if the sim is missing my key release 
then the AI thinks I am putting it to the extreme…
Since SU IV it does when you are trying to overpower the AP.
On all the larger aircraft I’ve flown you need considerable force to disengage the AP, but you are not able to significantly change pitch or roll without disengaging it.
@PZL104 you cite an earlier version of my text, please keep in mind my submit was about keyboard input, as is this topic. With keyboard you don’t get that override. The AP behaves better when you use a stick. With a keyboard, you can’t really change direction either, but… that is because you’ll be punished much more when you try to work against AP !
Thanks.
Unfortunately you will be sighing a lot more because such statements will never go away 
Not just for this game but any game and also for hardware related stuff.
I usually get games for $10-$20 during Steam or Ubisoft sales. This game was £110 ($155) which is not small money. So when you drop this much cash on a game and the AP works fine (even after the latest update) but then one day later for no apparent reason goes ballistic it is annoying.
It is just an expression of frustration and harms no one.
That is correct, it is not disabled. What caused the problem here was that I had a stick plugged in - but the sim also keeps the keyboard controls for the primary flight surfaces active. And each time I was jabbing a view hotkey I was unknowingly commanding deflections of the rudder, ailerons etc.
Now if the game had a pop up when it detected a controller:
<Hey we see you got a joystick do you want to turn off the keyboard flight inputs while the stick is plugged in?>
…I wouldn’t have had this issue. Its a bit of a small chore but I went in to each one of the keyboard control assignments and deleted them all and that immediately fixed the issue.
The problem wasn’t with attaching the stick, but that you were able to bind new bindings to those keys without being made aware there was another binding on them that could interfere.
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When I try to add a new key to a function, I get a warning
that the key is already defined for something else.
I guess they rather ignored the warning. It’s there (in red, iirc) whenever you assign a key.
No it just shows that people easily jump to conclusions that they are not at fault while they are.
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Yes - I wish the game addressed the latter part of your reply when it detects a controller is plugged in. As things stand (unless you delete the bindings) the game keeps the stick active AND the keyboard primary flight control keys active. So you can turn left by using stick left or press numpad left arrow. There was also some confusion over the 2nd column in the keys setting because I was assigning view hot keys to where the game had a primary control surface hotkey mapped.
People have all sorts of combinations of peripherals connected and use them depending on the aircraft used.
It’s not a bug that you can have input from multiple peripherals bound to the same action and in fact this is how most games work.
I’d be annoyed by popups asking me about my controls whenever I plug something in or out and I intentionally want to be able to control some things using the keyboard additionally to the stick.
But again, the sim explicitly prompts you about conflicts when changing assignments, you seem to simply have ignored that warning. That was the root cause. Just be careful with the assignments and you won’t need anything changed in the sim.
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You are correct, when in the key assignment menu the game does warn of that but when I set up the view hotkeys on the numpad in the 2nd column I couldnt recall a warning. Maybe its because I was setting up cockpit cam view keys and not flight control surface keys
Warnings are always overlooked. I’d find it more sensible if MSFS would just not allow double assignments. Just accept the last assignment and clear any others referring to it. When a function like elevator or aeleron is being assigned as stick function, MSFS should clear (override) its keyboard setting. When I try to assign a double key it should accept it and clear the old setting.
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If you check the default assignments, there are many duplicates which make sense since they apply in certain scenarios only.
For example, assigning external view movement is independent from the cockpit view movement and you can use the same key that moves your external view to do something else while in cockpit.
Limiting one key to one function would definitely break existing intentional behavior for some of us.
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You’re right, maybe my rule should apply only for settings shared between keyboard and stick sections ?
Double keys should be allowed, but not keyboard/stick mapping the same stuff ? It’s not only AP, in manual flight, using a stick and rudder peddles, you don’t want to risk your cat walking over your cursor keys !