I just reproduced it again so I can answer your questions:
Windows 10 64bit
are you loading torrents with the 'load transfer' window?
If you mean "Add new transfer", yes.
are you checking 'apply to all' and clicking start?
Yes, I am assigning a category and I do check the 'Apply to all' checkbox.
if so, it seems that it is using the trackers from the first torrent you are trying to add and applying them to the rest of the torrents you are trying to add.
Yes, first torrent's trackers are assigned to first and second torrents.