Hmm. That is the 3rd echo, correct? It looks fine to me, but it really seems like tedana masked out those low intensity values towards the center…even though that don’t look excessively low.
tedana has a mask option (Using tedana from the command line — tedana 0.0.12+0.g863304b.dirty documentation) --mask somemaskfile.nii.gz that you may want to try. I’m not sure if fmriprep automatically gives you some mask choices, but that would be my next step. I tend to use an automask (in the AFNI 3dAutomask sense) from the first echo - includes brain, perhaps a little bit of skull, but excludes areas outside head and with extremely low signal.
In fact, tedana should have produced some mask files - I assume those look like the beta maps there - missing a lot of brain?