Findmypast probably obtained the same set from the LDS as did FreeBMD, but it may depend on the date when received. Presumably the GRO still has any handwritten ones which existed, but not available to check. If the LDS had filmed them, they should have reached both databases, so if both have the scan missing perhaps it was never scanned. Having watched the LDS at work doing some filming (of card indexes) in the 1980s it would not surprise me if they missed the odd one! This comes to light in FamilySearch occasionally.
I think there is more than one version of some scans on FreeBMD but I have never checked systematically. I just try to avoid the very pale ones. There would always be room for errors when indexes were typed or typeset.
Some of the worst seem to be when they filmed a carbon copy of a typescript, 1920s & 1930s, and nobody had cleaned their typewriter keys, so they filled with paper fluff. (Requires methylated spirit and an old toothbrush!)