Uh... no, I don't think it is a commonly misused phrase.
To flagellate is to whip or punish oneself painfully to atone for perceived sins. Basically cause yourself pain to make up for your own mistakes (think Dobby the house elf in Harry Potter).
There are any number of other words I think you intended to use, including one that starts with F but is very crude (no it's not 4 letters) and would probably get your post Skuzzified (for scatalogical reasons).