Abnormal activity has been registered in/on my phone number, which is why it's suspended.
Strangely, both "in" and "on" can work in this sentence, as well as "with". All three prepositions are fine, but for different reasons.
"In" works, because the phrase "your phone number" can stand in place of "your account" as a free substitution. Abnormal activity has been registered, that is-- written down, in your account, using your phone number. So this works.
"On" works, because "your phone number" is a label or name that can have aspersions placed on it, such as an accusation of abnormal activity. "Suspicion has been placed on my good name" is a parallel sentence that works for similar reasons.
"With" works, because the abnormal activity is associated with your phone number.