If no other source is available, then one or two frames can be fixed by copying neighboring frames. Use the location of the red frames in the export file to help track down problems in the source footage.
This issue is not a failure of the export process, but rather an indication of a problem with the way the source footage was encoded. When Media Encoder encounters frames that cannot be decoded, it inserts red frames in their place.
The red frames serve two purposes. First, they keep the audio/video sync intact. Second, they make it easier to track down the location of problem frames. When a frame cannot be decoded, it is logged in the Events panel.
In the CC version, more strict format constraints were implemented, allowing the software to better detect and flag file corruption. In past versions, these problems could have been missed, causing crashes or failures when encoding the final project.
The red frames occur most often when using MPEG-based footage, and often indicate a problem with the GOP structure. Occasionally, with MXF files in particular, the footage could play in another application like VLC without any issue. The MPEG stream is intact, but the MXF index table was written incorrectly when the file was created. The software can't locate the proper frames according to what is specified in the index table, so it replaces those missing frames with red frames.