You will be making a "privacy act" request, so there is no fee. One of you should apply and the other should authorize release of their personal information as well - submit both forms so that the ATIP office won't redact out information that is private to one of you.
According to IP 8 they may refer cases to an inland office due to:
I suppose this could include an A44 report investigation (e.g., if you are not in compliance with the residency obligation) since if you are not in compliance you won't be eligible to sponsor, but from what I could tell in the processing manuals (IP 8 and OP 2) CPC-V should have handled a sponsor eligibility issue. If you are not under a removal order, your time in Canada does count towards your residency obligation at least.
There's some issue and the electronic case notes (do NOT order a physical copy) will tell you. I'm not sure, but I think FOSS might be dead now, as the goal was to switch everything over to GCMS ("Global Case Management System") rather than the old two system model (FOSS and CAIPS). When you complete the form, you will be asking for "electronic notes" and they will send you the relevant information.