I have an Advanced Autoclave II producing Raw Carbon Fibers. Once the output is full the Autoclave does not stop producing, instead it simply voids everything it creates.

Will be fixed by the GTCE update, adding to 1.3 for now.

Also have that problem. I tried all MV to IV Auto-claves in creative and they all failed to backstuff

Technically not a bug, raw carbon fibers are a "secondary output" so the autoclave is voiding the excess because the "main output" isn't full. but since the "secondary output" is the "main output" the machine will continue to burn them infinitely until it runs out of either input. Now whether Damien meant for that to be the case or not I have never seen an official statement on that, but just wanted to let you guys know (:

It's a GTCE thing, fixed in the new GTCE release, I believe.