Is it possible that the certificate number can be different than the one the company provided?

Hi. I have two IRP5 because I worked for two companies during FY2014/15. Upon completing my e-filling, I realized this at the certificate number on the system (SARS website) is different than the one the company gave me.

Is this possible and can I change the certificate number manually?

You can yes, but they will audit you so be prepared to submit the IRP5's to SARS when requested to do so.