Do you have anxiety? To me it sounds like you may. I'm guessing that this is involved here but because we don't know, you should see a doctor again. On the plus side, since an internist has said it probably isn't DVT, that's good news!! Whomever prescribed the BC, that is who to call. And do talk to someone about your anxiety. This may need to be considered as something to work on to overcome health fear that is unfounded. But first, make sure it's unfounded. Let us know what they say!
(ps/ DVT IS the biggest concern when taking birth control pills and the person who prescribed them is the best to talk to about that.)
Sounds like very minor pains that you would normally ignore if you weren't so worried that it is DVT. Since the internist said there isn't anything wrong, then try to relax and not examine your body, and forget about them and they will likely disappear.
There are about 5,000 diseases and conditions that a human can get, so there isn't any reason to focus on one like DVT - life is too short to spend it studying all 5,000 after an internist says he doesn't think there is a problem so no reason to study one either.