Puting in many items close to eachother not being a stack, for instance pressing q fast rather than toss a stack from inventory into an obsidian pipe, can dupe items if you break the pipe in a corner at a perfect timing (that gets easier the more items you toss in).

bug reports go here:
http://mod-buildcraft.com/forums/index.php?board=2.0

the github issue list is for who is fixing/ working on what