It seems this issue happens any time I open a text file from the file manager or desktop, if gedit opens into a maximized state. When I'm scrolling down, either mouse scroll or dragging the scroll bar, it won't go to the bottom of the document. If I use the arrow keys, the cursor will go down to the unexposed lines and if I type something below what's shown, the lower lines pop up.
Update: Changing the window by maximizing, minimizing, and even changing to another window and back, will make it scroll properly again.