My most questionable design decision: adding convergence where it didn't belong.
... Yes, I expected this to need explanation.
My main project, in its old form, included a chapter wherein you and a bunch of ally (green) units defend a fortress that's under attack. The objective was simply "Survive" and the chapter ended when the commander of the ally units was defeated and the player characters decided to run after that. However, in case the player got the bright idea of using a mounted unit to rescue the commander, the chapter automatically ended after eight turns (the enemy blitzes the commander hard before then so if you do rescue him it's actually pretty hard fending off level ~10 enemies in the front when you're supposed to be in the back fighting the level ~2 ones). I got the bright idea of inserting an Easter egg of sorts for those who had had the gall to defend or rescue the dude for eight long turns.
This is where I got carried away.
The next two chapters differed pretty substantially based on whether or not that commander survived until turn 8, with everything being things that would not be affected whatsoever by whether or not he actually died. You got different items from villages, recruited units in a different order, and enemies spawned in different formations. What had seemed like a brilliant, subtle gameplay variation spiraled out of hand to become an arbitrary clusterfuck which only resulted in people asking "why did I get the pegasus knight instead of the mage?" or "how do I get the archer to have the archer-useable dagger instead of the longbow?". To everyone but myself, it seemed random and poorly thought-out, and I didn't realise it until I finally scrapped that version of the project and restarted on a new rom. This time, I allow the player themselves to choose what to do in what order rather than throwing it at them in xyz order based on conditions that have nothing to do with what's being thrown at the player.
I think I may have just been slapped in the wrist by this very thing, actually. I made some innocuous Nightmare changes to my rom, suddenly it was incompatible with FEditor ("thread error" when trying to open or something like that), then I noticed that some bytes at the end of the rom had been changed for some reason. I went and changed them back to what they were and everything works perfectly again.