Usually, when an application is returned, the entire application must be re-submitted and...sometimes that includes the fee.
Since someone (or a robot) determined that the application was not complete, they may feel justified in charging for `their time' to have found the mistake.
Prior to the change a couple of years ago, mandating that all applications are submitted online, there was also a risk that one (or more) of the paper forms may have been updated after the original application was submitted and those that resent the same (now outdated) form(s) had the application returned, again. The online only system would seem to have, at least, eliminated that problem.
You might call IRCC and hope you can reach a human. One that actually provides an accurate answer!