Given the data you have provided (no penetration, no ejaculation, clothes on), there is no chance that your girlfriend has somehow conceived.
Spermatozoids in semen have to enter the vagina, then the cervical canal, through the uterus in order to reach Fallopian tubes at the end to fertilize a released egg. Because clothes cannot allow the semen to pass, conception with clothes on is impossible.
Your girlfriend, however, might want to visit her gynecologist to identify a possible pathological condition that is causing her period to be late.
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