I am not sure but I think this is a problem on the 500 series scanners when listening to mixed mode Motorola systems. There are some settings in the "Super Expert" menu which affect the Motorola End Code detection and I have played with them alot a long time ago in order to try and fix this issue on the system I listen to. I was never able to fully cure the problem and just learned to live with it. I think the problem might be that the scanner does detect the end code when an analog voice signal ends but does not correctly do so when a digital signal ends. At least in my case, the problem happens during busy times when a digital voice signal ends and immediately that voice frequency gets assigned to another (in my case, usually analog) talk group - then I hear the wrong traffic from that analog signal while the scanner thinks it is still on the previous talk group. On the system I listen to the talk groups are all separated into exclusively either digital or analog so it's pretty easy to detect this issue. The Unidens have separate end code detects for analog and digital which may make them work better at this though I don't have one to play with so I can't say for sure. Also, I don't listen to many pure P25 fully digital systems so I can't say if the issue is also a problem on those but my guess is that it probably works better on such systems; I think it's the mixed mode Motorola systems only that give it problems.
Still, you can try and see if you get better results by playing with the available settings for the Motorola End Code. I wasn't able to make make the problem go away completely myself but you can give it a go. You can go into the super expert settings by pressing PGM-->FUNC-->GLOB and scrolling down to the "SubaudDelay", "M36 ET Patt" and"EndtoneMot" and note down the current settings on those and then play with them to see if it helps you. I would leave the "M36 ET Patt" setting alone - I really have no idea if other "patterns" are used and since there would seemingly be many possibilities it just didn't seem like a viable thing to play with to me. But you could mess with the other two and see what you get - again, just make sure you note what they are currently before you mess with them in case you wind up making things worse and need to go back to what they were originally.
Also, if you have WIN500, the settings are in the "Extended Settings" tab in the "Motorola Trunking" but with different, slightly more descriptive labels.