Back again. Well, as is always the way, I couldn't reproduce this effect at all. I note your comments Phil, about water mineral content etc. However, we are on rain water here and it's filtered so doubt there is anything in it to cause mould growth.
From memory it always seemed to be under the wood when clamping the leather into a shape while wet. It could be something about the leather as it is inconsistent as to when it happens. Or could be fine metal dust contamination in my workshop from knife making.
I will attach a couple of photos in which there is definite staining. However, in this case it was caused by the carbon steel blade inside. This set up was a trial run mock up for a dirk I am building as I needed to get sizes and a pattern worked out for the leather plus the stitching and process to get it all to go together. So, not worried about the rust bloom coming through as it will end up in the scrap bin anyway.
But, as you say, when wet moulding a sheath to a blade it is always wise to wrap it in several layers of cling film or coat in vaseline, or both.
As a tip on vacuum moulding, the leather wont dry in there because it's a vacuum. So once the leather has pulled into the desired shape, release the vacuum and remove from bag to dry. But don't remove the blade or other former being used until the leather is dry.
I also find that the internal pattern on the vacuum bag (that allows the bag to evacuate the air) will imprint a pattern on the leather. If that is not desired, then I cut a piece of thick polythene and place it between that side of the bag and the leather. I use what we call in NZ, builders plastic: a thick black plastic used under concrete etc to block water and rising damp. It's smooth and also very useful to stop clamps and blocks etc sticking to the work when glueing up as PVA and epoxy wont stick to it.
Probably those thick plastic document sleeves will serve the same purpose.