Problems with plan b pill. kidney infections and missed period. with a negative preg. test.?

my girlfriend and i had and the condum broke. we used a plan b pill right after it happened. she had just gotten off her period when this happened. she used the pill and started her period the next morning. she then came down with a kidney infection and was on antibiotics and pain relievers for a week. with the combination of the plan b pill and the infection shes late for her cycle. i know that the pill throws off the cycle and so would a kidney infection. shes a couple weeks late now. we took an EPT digital test it was negative. could she be pregnant or just having a messed up cycle?