E.g. apps not being able to see other apps by default has caused issues for some screen recorders or screen-sharing software. Or screen readers from seeing inside apps.
Or apps not being able to see keystrokes when the app isn’t active, impacting global shortcuts (say, for example, you’re a streamer who uses a hotkey to change cameras in OBS)
A lot of Linux stuff was written with the expectation of there being zero security safeguards. With Wayland, that has changed and it’s causing issues.