Copying my response:

Speaking from a position of profession, this is not "regular procedure". Yes, you do get vetted, but vetting does not include intercept of private communications, whether talking something regular like a SSBI or a senior leadership position being filled. Vetting involves publicly available and personally volunteered information. While the government can obviously monitor official government communications (eg on a gov phone or computer), intercept of US person's private communication (as in Flynn's case) requires a FISA warrant. That FISA warrant has been outlined in several articles on this subject. A FISA warrant on a US person's communications arises not for routine counterintel purposes but because there was suspicion of foreign intelligence value (the difference here is one is preventative and the other is reactive). It is not routine for National Security Adviser or anyone to just get a FISA warrant slammed on their phone. Several articles on this subject have made it clear this is a result of existing collection on Russian ambassadors creating red flags.