There is no way that “happens on a lot of add ons” unless it is supposed to happen. I have many add ons and they never have an issue if the aircraft and AP is setup correctly.
I think you need to give a lot of details or better yet, a video of what is happening and what you think should happen.
In answer to your question. I guess if you only have obscure and really poor quality free aircraft maybe editing the files might be needed. I don’t use those myself. In that case you would have to download the msfs SDK and learn about editing aircraft files. There is nothing you can do with the AP itself seeing it obviously works well with the default and payware aircraft.