Suppose You have a pdf 'X' having many no of pages. Now you have designed/modified anothe pdf of having one or many no of pages and want to insert it into the 'X' pdf. At this moment, if you will make open both the pdfs, then it will show you this error. Do one thing, just close the modified/new pdf file. And then use Tools menu to insert pages from file. It will work.
As I understand it, you have used the Document>Replace Pages tool, or the Document>Insert Pages tool. The former is useful if you are replacing individual pages, particularly if you have added markup. The markup (like form fields) will remain if you use the replace option. If you can't save the file, then just use Save As. I often use Save As to overwrite the current file. The advantage of Save As is that it strips out the old changes that Save keeps. If you use Save, the file will often become bloated. You can also do a Save As to a new file name and then delete the old file when done.
I don't have an answer to why Save is not working for you as it should, unless you are playing with a PDF/A file or such, or the file is protected from changes (security setting -- You can often make changes in the document and don't find out until you try to save that it is locked). So check for either the archive format (PDF/A) or security setting. That is all that I can think of that is blocking the save.