Edit: Issue not just from tinkercad files.
I've only had this issue with parts created at tinkercad.com. Possibly something their software does is to blame, but the strange thing is that the parts are fine when loaded into slic3r or cura. That is, they are not inverted. Is there a setting that could compensate for this?
For now I will create parts some other way, but it's a super useful site since it's really easy to make simple parts.
Here's an image that makes it easy to see the problem, sorry it's a little blurry.