It depends on what happens when there is an IO limit fault. If the corresponding IO operation fails (is blocked/aborted) then yes, that could definitely cause what you’re seeing.
If possible it would be better to throttle operations that go over the limit (make the offending read or write take a few extra milliseconds instead of just failing completely).
The WP/CP update process is not designed to deal with servers that may fail when writing or reading files. It could be made to deal with these conditions but that would be a pretty major undertaking.