Looks like the red channel is somewhat diffuse staining, it could be that the low contrast leads to the stitching issues.
If I recall correctly the stitching is done on the first channel imaged (or the focus reference?), perhaps changing the acquisition order dapi>whatever is in red will already lead to better results (don’t quote me on this one), when using '“online” stitching (default).
There is also the ‘‘offline’’ and ‘‘fuse active’’ options under ‘online-processing’ that may improve the stitching results.
You can also restitch post-acquisition with zen, and then only select the channel with good/best contrast.
There is some additional info on post-acquisition stitching in the post below: