The X just means that AMCAS made some sort of correction to that course. Most often they disagree with your course classification and reclassify it (e.g., you list neuro as bio but they move it to psych, etc.). Double check those courses and make sure they're correct.
The courses are still used to calculate your GPAs. It could impact your BCMP GPA if they move a course in/out of a BCMP classification.