Measure voltage using transistor with strange behaviour
You should use a P channel mosfet controlled from a low side BJT or N channel MOSFET. What you have at the moment is an emitter follower and that does indeed act like a regulator. Try something like this: -



Basically, when you want to measure the battery voltage, you use a spare IO line to activate the BJT. This then turns on the P channel MOSFET and delivers the battery terminal (through the on resistance of the MOSFET) to the potential divider.

See also this page which makes your question a duplicate.