makeBins.R generates spurious bait fragments

the output "baitmap" file has more fragments than the corresponding input file:

Rscript makeBins.R --baitmap bug.baitmap --output_prefix bug1 --binsize 5000 bug.rmap
Creating 5000kb bins...
All restrictions fragments except baits will be binned...
Binning rmap...
Rmap has been binned with 5kb bins. Results saved in bug1_5kb_sol_baits.rmap .
Editing baitmap...
Done!

wc -l bug.baitmap # input file
100 bug.baitmap

wc -l bug1_5kb_sol_baits.baitmap # output file
132 bug1_5kb_sol_baits.baitmap # 32 bait fragments out of thin air

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