I thought I had this same issue, but when I started keeping track of my xp to edit the lost amounts into my save file, I realised what was actually going on.
Say you had 100,000 xp before a raid and during the raid you got 5,000. The end of raid level progress bar would show you going from 105,000 up to 110,000, before the character screen correctly showing the 105,000 figure it should have been, so you never actually lost that xp but it was certainly pretty confusing as the end of raid screen essentially counted it twice.
Would keep an eye on your xp stats over a couple of raids and see if you've got the same thing happening.
