Hmmm. I've never see that message before.
Here's how Compare Docs works: Adobe FrameMaker: Compare Documents (Part II in the Editing Series) - Rocky Mountain Training
Now, taking the message at its word, here's how flow tags work:
- The flow tag appears in the status bar, in the lower left corner of the Fm window, right above the Windows start menu. Start by clicking in the text on page one and note the flow tag in both files. Are they the same or different? Flow A is the default, but even if you are new to Fm, I can't imagine you changed the flow tag without realizing it.

- To answer your question, you can change the flow tag by going to Graphics > Object Properties > Text Frame > Tag.
Do you have multiple flows in the files? Or in one file?
Also, at the bottom on the link I posted above, I noted that Adobe Acrobat Standard/Pro (not Reader) has the same feature. That may also be a solution for you if you don't figure out what is going on with FrameMaker.
~Barb