There is defiantly a challenge with some plugins.
I’ve had issues with “Waypoint” because of how it functions. Going between mobile and desktop when they where out of sync, waypoint creates files if not there so this can confuse sync software for sure!
Some polish, extra UI around enabling/disabling it. Syncing is a tricky thing! Usually my changes ends up leading to 1000’s of files moving and added at a time so syncing takes long and can get stuck BUT luckily I’ve learned enough from plugins messing up things to avoid them or use them on smaller vaults until tested.
Good luck!