Yes. “It does that.”
Switch to the latest experimental build of the FBW A320, which has a custom flight plan manager which has more or less fixed these weirdnesses (as well as hundreds of other improvements to the realism of the A320). You’ll find STARs in particular to be much more reliable and you can actually remove errant waypoints from the flightplan now.
You can install the three different versions of FBW from their excellent installer, so no need to mess about unzipping files.