To reproduce:

1. Create a stack of 4 extended or potent fermented cider bottles
2. create a fluid tank from OpenBlocks (does not happen with Tinkers Construct fluid tanks, have not tested other mods)
3. holding bottles in hand, right click to empty into OpenBlocks tank
4. Observe: one bottle of cider in tank, one empty bottle returned.

edit: potent,

More notes: milk products also suffer this problem.

Problem does not occur with Thermal Expansion's fluid tanks. Seems to be a specific problem with OpenBlocks tanks, which is a shame as I like their look.

I've gone through the OpenBlocks code and this is due to the way that they process the bottles. Not sure that there is anything we can really do to change it other than make it do the bottles do not stack.