Ok. So couple of things.... Your sponsor is Canadian, yes? He has citizenship? If so, don't worry too much about it.
Here's why:
When he immigrated, they created a record for him at that time, based on his parent's details. That record is forever linked to him via UCI. That means, the number on his passport, his citizenship card, etc all will forever be linked to his file. They know very well who he is.
If you're not placated by this assertion, you can easily go to a MPs office, explain the trouble with CIC, give them the ID, and have them try to sort it out.
If it was me, I would rest assured that it's a systems flaw, and that he is tied via UCI. To test, try logging into ECAS using that UCI as identification.
HTH!