It looks like this MPEG-TS stream is not properly aligned. Some muxers do not properly start each new RTP packet on a new MPEG-TS sub-packet. This can lead to this warning in the logs. We do not have way to work around this. What encoder is being used for this stream?
It should but this is MPEG-TS over RTP. With MPEG-TS over RTP a single RTP packet will container more than one 188 byte MPEG-TS packet. Some muxers will not properly start each RTP packet with a new MPEG-TS packet. They will instead break 188 byte MPEG-TS packets mid-packet.