Someone was nice enough to do a lot of testing and found a couple of interesting bugs:
Use amount larger than 127 for /kci give: command.txt Fixed
Double-clicking on a stack in an input slot of a custom container: vanish.txt Fixed
This one doesn't really make sense. It occurs when right-clicking an item in a custom container:
rightClick.txt The reporter claims that this has been fixed already, but I never managed to reproduce it

1 more, quoting the reporter:

so i have an item exchange for 10 items to 1. when i fill my hotbar (9 slots) each with exactly 10 items and i right click. i only get 1 item instead of 9

TechWizzart fixed it
small one from someone else:

when I try to repair something in an anvil for the first time, (the scout helmet from guaz pack for example) it works fine, but the second time I repair it doesn't happen anything. I created my own items too and its the same problem, the console doesn't drop any error.

I couldn't reproduce it. Waiting for more information from the reporter

The reporter for the last remaining bug hasn't replied yet. I will close this issue until we have more information.