I still have the same problem in SNAP 5.0 (SNAP Desktop/Engine implementation
version 5.0.4) with Sentinel-1 Interferometric Wide swath (IW) images.
It seems that the multi-resolution nature of Sentinel-1 causes the problem.
See for example:
https://senbox.atlassian.net/browse/SNAP-729
I think the internally created mask has product-width, which corresponds to width of the
Deburst-image for Sentinel-1 IW. So you will never see this mask within one of the separate
IW1/IW2/IW3 Bands.
After creating a Deburst-product (Radar/Sentinel-1 TOPS/S-1 TOPS Deburst), the Mask Manager
was filled as expected.