itch.io has a binary patching system in place. It may not have taken because the previous install basically 'failed' so the binary patcher likely just thought "well this is totally screwed up you'd better download the entire game again!". For future patches you should in theory only get delta patches
If you have any bugs, create a new thread and report it. Please ensure you try to be as verbose as possible. If you can include both a save game that is affected and any logs that would also be helpful. Also include your basic system specs (CPU/GPU/OS)