fMRIPREP is not working for certain scans

I am running fMRIPREP on my dataset. I automated the scripts to generate a script for each participant. Each script is run on the argon cluster. It worked for the majority of the dataset, but a few of them keep crashing for unknown reason. Everything has the same format, file size, structure, etc. The error log just gives me this. I would like to fi this without having to update to a newer fMRIPREP installation to avoid rerunning the entire dataset. Any ideas are appreciated.

You are using fMRIPrep-20.1.1, and a newer version of fMRIPrep is available: 22.0.2.
Please check out our documentation about how and when to upgrade:
WARNING: Version 20.1.1 of fMRIPrep (current) has been FLAGGED
(reason: Functional outputs in standard space can be wrong depending on the original data's orientation headers - see
That means some severe flaw was found in it and we strongly
discourage its usage.

Hi and welcome to neurostars!

Are there any other relevant logs, subject output HTMLs, etc? The flagging notice should not cause the job to stop.

Personally, I would reprocess the dataset rather than using a flagged version. I would have more peace of mind when analyzing the data.