Could be there was a tower issue in your area. I had this happen before and called Sprint on it, they confirmed they had malfunctioning towers that normally handled the SMS/MMS and secondary towers handled the messages which caused the delay/delayed time stamp.
It happens when the phone is roaming and you receive a message. It can't get the correct network time reference, so it defaults to UTC (Coordinated Universal Time) because that's the universal world time which all time zones reference (and the time that SMS uses).
It's not the app specifically, though there may be other apps that will reference the phones internal time when time stamping messages, but I don't know of any.