Wrong column occupancies on big alignments

On big PFAM alignments, e.g., PF00439, column occupancies are wrong for very low occupancy columns. Occupancy shown while hovering over the occupancy annotation track is wrong, sometimes greater than the number of sequences of the alignment. Also, consensus sequence can't be viewed on those positions because there is a white bar covering part of the amino acid one-letter code, possibly a consequence of the wrong occupancy value.