It turns out in my document, some of my pages have a master text frame and others don't. Many don't. It must be the way I created the frames, accidentally creating independent frames. Is there a fool proof way not to accieentally create independent frames and is there a good way to make sure all these pages with independent frames are turned back into master text frames?
What I can do is delete the independent frame, then link the previous frame to the inside of the master text frame (I think I used to drop the link on a ruler too often and that creates an independent frame that is in most cases indistinguishable from a master text frame). This is tedious to do for the entire document. Is there an easier way?
It sounds like you understand what happened. Clicking the place gun cusror on any type of guide will ignore your master frames. Overriding a master text frame before placing the text and Shift-clicking in the overridden frame will also ignore the master frames on subsequent pages.
The bes thing you can do is keep your eyse open to watch the shape of the cursor. If ID is going to use an existing frame the cursor will be surrounded by parentheses and a new frame will use a cursor with a square upper left corner. You should also develop the habit of clicking in empty areas away from guides if you are using existing frames -- you don't need to click at the top of these frames.
It's also possible that you did everything correctly and you are working in a facing pages file and at some point added or deleted a single page somewhere other than the end. That would cause all following pages to switch sides and master objects would be reapplied behind any overridden frames.
There is no easy way to deal with extra frames. If they are not causing a problem you may be able to simply ignore them.