Why Does Stroke Do This?

[RDonadio]

I have seen this issue occur a few times. 

I am new to logo making and made this logo. After simplifying and using Pathfinder to merge the shapes, I don't see anything wrong with my paths. I will attach two images, one with the logo, and one when I try to apply a stroke:

[Monika Gause]

There could be duplicate anchor points in that corner.

[Jacob Bugge]

R,

In addition to what Monica said, there are (also) unneede/unwanted Anchor Points on what ought to be straight segments, 5 of them being directly visible in the screenshot.

That white path ought to have only 9 Anchor Points at the corners, and any number beyond that makes it less clean.

You can remove the visible ones, and then look for the remaining one(s) at the corners. One way is to deselect, then Click each (top) Anchor Point with the Direct Selection Tool and press one of the Arrows on the keyboard for an incremental move to reveal whether there are two, then remove the unwanted one if any; you can reverse the incremental move; and Ctrl+Z for Undoing is your friend.

Stroke only does what you ask it to, and sometimes it can help discovering discrepancies that can otherwise cause trouble.