That is the null character, in a format (which Vim uses a lot, as you’ve probably noticed) called caret notation. Basically, somehow you’re getting bytes full of zeros into your file.
Since we don’t know what your utility is doing, if it’s the culprit, you’ll need to show us some code if you want us to help. Otherwise, if you just want to remove the characters from your file, use a substitution:
%s/<Ctrl-V><Ctrl-J>//g
Ctrl-V marks the beginning of an escape sequence. After pressing Ctrl-J as well, you should see ^@ appear in your command. Thus, as you guessed, Ctrl-V, Ctrl-J is one escape sequence for the null character.