The bottom of the bottle

Instead of poking the needle through the middle of the rubber part of the cap try near the edge. Tilt the vial slightly so the part you poked is slightly lower and pull back the needle so it just clears the rubber on the inside before you pull on the plunger. It's tricky and you risk dulling or bending the needle -- but if you are a cheapskate like I am that last drop will bother you if you can't get it out.

Rotor, are you turning the bottle upside down when filling the needle? Also are you injecting the equivalent air into the bottle before trying to withdraw the med? For instance, if you want to take out 5cc medication, put 5 cc of air into syringe and inject that into the bottle while it is right side up, then tilt upside down to get withdraw medicine. as Peter says pay close attention to where how far the needle is in, and only have it just past the stopper when withdrawing the meds to get every last drop.

May take some practice but if you ask real nice I bet that your doc's nurses will give you bottles of regular saline to practice with and also may even provide some teaching on this to help you perfect your technique.

Your method is okay but more work than necessary.