I am using version 0.3.5.1 and am not able to extract or insert fluids using Thermal Expansion's tanks and the Ender Bucket (in either Output or Input mode). I tested with a few fluids to see if it was isolated to just one but no liquids were able to be used. Of the fluids I tested were water, lava, and several fluids from MFR, Tinker's Construct, and TE.

However other tanks function correctly using Thermal Expansion fluids.

For reference this was happening in the mod pack Sky Factory 2.

There is a little quirk with the TE4 tanks. They do work if you target the blue input side of them (so top or bottom of the tank, when it is set to blue aka input). I guess I could add a special case for those tanks and make it fake the action to always happen on the top of the tank (the top can't ever be orange, aka output, right?).
There are also other improvements to the bucket in my dev branch already, for example the ExU drums work without requiring setting the bucket to input or output mode. Not to mention the pretty sweet new ability of cough censored cough ;)

I'll leave this issue open until I release the next version (0.4.x ?). I probably won't fix this for the 0.3.x branch anymore, since it does still work, you just need to target an input side of the tank.

This is "fixed" (or more precisely worked around) since commit 87ce3fe (will be in release v0.4.0).