There's no need for correcting the key, or for any work-around - even though it puts the warning in the log, it still updates your catalogs and downloads/installs packages just fine.

If you could post an exact log (and perhaps what repositories you have enabled) it would be easier to figure out why exactly this is happening to your device, but I imagine it has to do with the fact that you have multiple different repositories enabled, and some of them contain the same packages. So it's detecting some wrong version of a package in one of the repositories, and ignoring it. I could be wrong, apt is by no means something I'm an expert in.