Is it a matter of pre-patch and post-patch ones not stacking together, or are new ones not stacking at all(even with each other)?
If it's a matter of pre-patch & post-patch, putting the pre-patch fish into a commodity deed, then breaking it, probably will fix it (much how non-stacking gold is fixed by making a check).
However, fish don't have to be stacked in quest crates, so it isn't much a matter - and fish steaks you donate to the library by number (regardless of the number of stacks).