Hi Brandyn,
Thank you for reaching out.
This is caused by some errors in your design where the edges are not connected.
When you upload the model, our model processing software tries to fix these open edges, unfortunately it caps them in your case.
You can easily check this yourself with the free tool called Netfabb Basic.
The STL file from your post.
After i click on the repair button in Netfabb it shows the yellow lines, marking the areas that aren't closed (the red parts mean the faces are flipped, but our software will automatically flip them)
Applying a fix shows that the edges are being fixed by capping them:
So how to fix: make sure the edges aren't open in your 3d software (connect them / weld them).
This should make sure our software wont cap them while trying to fix it for you