Is this one of the enlargers which places the filters on a surface, or does it go into a filter draw? If it is on a surface, a diffuser or condenser for example, then think of keeping the filter out of contact with that surface.
Alternatively, to change between formats there is probably an adjustment to be made with the head. Is that adjustment correct?
To check for oddness in the negative itself, simply turn it 180 degrees and if the marks stay in the same place relative to the enlarger then it's the enlarger system (unknown what precisely of course), but if it moves with the rotated neg, to stay the same place in the picture, then it is something connected with the neg.