If there are masked pixels in the overscan, the MEDIAN_PER_ROW overscan correction code generates a warning:

python/lsst/ip/isr/overscan.py:344: UserWarning: Warning: converting a masked element to nan.

 rowMedian = afwMath.makeStatistics(row, fitType, self.statControl).getValue()

Please remove this.  I think the simplest fix is row = rowrow.mask.data[0] in collapseArrayMedian, but there may be other occurrences.  A better solution might be to stop using np.ma in favour of using stack-native code everywhere, which understands Mask planes.