In my experience you cannot use antibiotics during reprogramming, but after you have your iPSC established you can use in case of contamination or to avoid it. Depending on the contamination level you can eliminate it, exactly as in other cell culture lines. I have treated them using gentamicin, keeping the other culture conditions. However, if you have huge contamination it´s not worthy to treat them because iPSC are most sensible them other cell types and they become very ugly and start to differentiate. Good luck!

In our lab we never used antibiotics during reprogramming phase but after the lines were established we used 1% pen/strep

I hate to say it but if you have a bacterial contamination, I believe you should carefully check all aspects of your cell culture practice. Clean and sterilize the hoods, incubators and be careful not to hover with your hands over open culture vessels when manipulating them under the hood. Try to pinpoint the possible source of infection, the weakest link in the whole process.

We routinely culture iPSC in E8 medium without any antibiotics and never had a contamination. If you need to use them, it is recommended to use lower concentrations (since there's no serum to offset their effect) but ideally, try to avoid contamination by improving the handling practice so that you don't have to worry about potential negative effects of antibiotics on your cells.