I am assuming you have already removed the video effect using the option in this image - right click each clip in the collage .
If this does not remove everything then you will have to do it manually by following the instructions in this image - note you will need the Effects tab and maybe switch between Movement Effects, Size and Position and Video effects to get all the effects that were added. You will then have to move each clip and readjust its length if necessary to put everything back as you need it.
I had the same problem with a slideshow - can you help with that? I put 4 pictures into an effect, then removed the effect, but one of the 4 pictures then started popping up by itself. The picture no longer showed up in any track that I can see, and I can not get rid of this picture. It shows up right on top of the pictures that are already in that spot.
Actually, it happened a second time. I now am not comfortable using any of the effects, which is a shame because this is one of the reasons that I bought this software.
It is likely that you have one picture superimposed on top of the other. Click the offending clip and drag it downwards, this should expose the other clip.
It's a bit of a longshot but I recall once tracing the cause of a similar mystery to the fact that the collage had used a surprising number of my 16 tracks, and when I scrolled right down I found the elusive clip.
Also, you might just check using Ctrl+8 that you are viewing the entire timeline, with nothing hiding away in the far distance.
Finally, occasionally I've had bizarre behaviour which seemed to be due to MEP somehow retaining a deleted clip in the cache. Try changing the cache options, using Program Settings > Playback. But I think that that only gave a spurious fragment of playback, not affecting the rendered movie. Maybe try exporting a short section including the mystery clip, and establish if it's 'real'.