Update: Ticket for the issue is now here https://github.com/galaxyproject/usegalaxy-playbook/issues/257
In short, until resolved (when the ticket closes out), set the destination cluster on the tool form as described in the ticket and the linked workaround Galaxy Help post: HISAT2 Not working
I never received an example Bowtie2 error but was able to reproduce the issue in directed testing. The last round of the testing is in a shared history link in the Github ticket if interested.
Mapping jobs will route to available cluster resources. My guess is that initially for both of you that the jobs were routed to one cluster, then later on the other. One works, the other does not at present. This will be a priority correction.