Hi IndoCan2014,
From your post I understand you've already communicated with WES to have your assessment package upgraded to FSWP. Correct me, if wrong.
If so, then you just need to inform CIC about this. Did they provide you any option on how to revert to them? If not, then email them this information.
Yes, this is a "known issue" if you do not choose the FSWP package in the first place.
No, this wouldn't result in rejection of your application since you've already taken steps to rectify the mistake. Now you just need to focus on intimating CIC about the change.