I am guessing that this is not the first time they have had a problem in getting your logs in a timely manner. The reason I say that is simple. If you were not a "repeat offender" on the log issue, they would let you sit, but wouldn't mess with your paycheck.
FWIW, I've got an acquaintance who lost a good job for just such a stupid reason. And he is very lucky that he just got in trouble with his company. He ran for MONTHS with NO LOG. Then tried to piece together where he had been to fake logs for the company.
If he had ever been pulled into a coop, he would have had major problems. But then he IS an idiot anyway. . .