Hi @TTP
IGV will not have your “custom” genome" fasta already indexed. But you can create a custom “database” key from your fasta both in Galaxy and in IGV, assign that to datasets, and view all just as if the database was natively indexed.
The error you are getting seems like you assigned some other database key that was already in Galaxy and in IGV – and your data is not actually based on that other database, so a mismatch error resulted.
This prior Q&A has many more details. The context is about an assembly result, but the basics are the same: how to use IGV with a custom fasta target/genome plus any other data that is associated with it (like a mapping result eg BAM). Opening Unicycler assemblies with IGV local - #4 by jennaj