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@mespilus
Natural stone staining when joints are sealed with poor quality silicone sealant is commonplace.
(The cheapest plasticiser for silicone sealants is normal conventional dimethicone silicone oil,
which is totaly unreactive. It remains labile in the cured sealant, and will migrate towards and into any porous surface). Cannot even be solved with correct priming of porous surfaces.
Reactive plasticisers are available, but of course are more expensive.
Sealant manufacturers instead turned to 'modified silicone' sealants, which have the curing mechanism of both high-mod, (evolving acetic acid/vinegar smell on exposure to atmospheric moisture), and low-mod, ( a couple of reaction mechanism, but broadly no-smell), but the polymers have better flow characteristics so require zero or much less plasticiser.
Did your tiler use 'silicone sealant' as the 'waterproof' tile adhesive?
The back/reverse side of domestic tiles is typically highly porous to ensure sufficient grab from water-based cementitious tiles adhesives/grouts.