This is behaving as most clients do. I get the same errors on cross seeded torrents in rtorrent as every torrent's set of data differs ever so slightly. If the torrent doesn't actually stop, ignore it, it just means you can't send the corresponding chunk that someone requested because it was overwritten with the chunk from tracker 2. Your client just reports the error and moves onto another request.
Example in scene releases would be a nfo getting tagged by a topsite script, tacks on a name to the bottom of the site it bounced through, few bytes difference between trackers, depending on where the tracker got it.
Rehashes result in which ever torrent you rehash last getting its version of the release, so all previous rehashes of the same release would report issues if that part is requested.
Q
------------------------Post auto merged------------------------
The only way to avoid these errors is to copy the entire release to a different directory and specifying tracker 2 to use that copy of the data. It will sync its differing chunks and no other torrent would be fighting it since it is its own copy entirely. This would use a lot of disk space, and manual intervention, unless you understand hard links.
Q