Could well be a fungal/mould issue which is due to water ingress and/or poor ventilation inside the bathroom. Did you use an anti-fungal sealant? Was it a major brand or one of the cheaper versions?
There are anti-mould/fungal sprays which MAY help if the issue hasn't penetrated deeply enough but it may require cutting out the offending areas and re-sealing with the proper stuff.
As an aside, you will need to sort any possible ventilation issues out if you have them because fungal/mould growth will re-occur even with the proper gear if you don't.
It was a bathroom remodel. They installed a new exhaust fan/does a great job. They were going to use mortar, but would not fit in size of window removed. Not sure what brand of silicone was used. I've got a call into company that did remodel now. Thanks for the info on the anti mold/fungal spray.
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