Internal Hotfix Builds - update from previous version possib

I just updated a 6.1.4600 site with the 6.3.5017 sitefinity.exe and went about it as usuall using the www.sitefinity.com/.../upgrading-your-sitefinity-6.1-project-to-the-latest-version documentation.

Someone it feels like some or all .dll were not updated to the newest version. 

So my question 

1) did something just go wrong?
2) can internal builds be used as we would normal builds for updates
3) could it be the internal builds just update some .dll that were worked on.

My guess would be 1)

Markus