Hello,

 Both of these are warnings not edge cases, where you as the user must ensure everything is correct. These reflect datasets where I have had little exposure and where it is possible that the solution is not robust

The weird protocol slice number reflects a sequence that was run with with H>>F. Presumably, the person who set up the sequence assumed that this would create descending acquisitions, but this is not the case. As Siemens notes: "Do not use the mode H>>F because this complicates the numbering and you will have to sort images manually in most fMRI post-processing tools. The excitation of the slices in this case also starts caudally with the highest image numbers counting backwards!" I would strongly suggest users follow Siemens recommendations, and I obviously have few exemplars where users explicitly disregard the manufacturer expectations.

https://marketing.webassets.siemens-healthineers.com/1800000001646277/f90d901c54b7/Flash60_HIDI_Slicetiming_Graessner_final2_KORR.pdf

Some Siemens Vida's had early versions of Siemens XA, which did not provide accurate slice timing in all situations. This is fixed by upgrading the scanner (I believe XA20 and later are robust). Regardless, when you see this warning you will want to inspect the slice timing values to make sure they are correct.