I've never (personally) had an issue myself, but I've seen others have a similar/same issue as yours.
It looks like there's a few things to consider regarding this error and I'm just going to paste some suggestions made by others that (hopefully) helpful for you.
1) WikiTree permits GEDCOM uploads of 2,500 persons or less.
Reference:
http://www.wikitree.com/wiki/Before_importing_a_GEDCOM
http://www.geneamusings.com/2013/12/adding-early-seaver-generations-to.html
2) If you've attempted to upload the same GEDCOM file multiple times, this could lead to some issues. You may/might/will need to delete/remove all the others (aka... clean up all the GEDCOM files), then try again.
3) If all else fails, add the "GEDCOMPARE" tag to this post to get the attention of those who may (hopefully) provide you with some guidance/help.
Finally, I if the above doesn't work for you, I can only suggest you sent a message about your GEDCOM problem to info@wikitree.com and explain the problem the best way you can for some guidance.
I wish you the best of luck! :-)
~Brian Kerr