You can make a complaint to another crappier (excuse my language) department about lateness of your ATIP request:
https://www.oic-ci.gc.ca/en/make-complaint-online
If you do make a complaint to them make sure you call them couple times to follow up or else Information Commissioner office ^^^ will also not care about your cause. Once they start the process then CIC ATIP officers will take action and send you the request.
As for your 2nd question, a lot of people have similar experience / files lost, delayed, not taken action upon, you name it. CIC is the most disorganized / dysfunctional gov org that we pay taxes for. Only thing you can do is email, call, reach out...