I wouldn't be too worried, it's natural for your gourd to take on color during the curing process and as you put it to use, the walls of all my gourds turned green upon curing and over time have all turned a deep dark green/black color. Just in case what you have really is mold, the best way to wash/clean a gourd is to wipe the insides out with lemon juice and some sort of abrasive scrubber.
As far as the curing process, did you scrape the soft insides from the walls of the gourd with a spoon or similar? Did you leave it to sit full of mate' for 24 hours? If you add flavor herbs or sugar during the curing process these flavors will kind of seal themselves into the walls of the gourd and lend a hint of their presence to everything you drink from it in the future.
In any case, the moral of the story is when in doubt, scrub with lemon juice
Protip on the preparation of yerba mate':
Put your mate' in the gourd and cover it with cool/room temp water, just enough to barely submerge the the tea and rehydrate it before you add hot water. This helps protect some of the more volatile compounds from being destroyed by the heat. In general if you make it too hot to immediately drink you are burning away a lot of the medicine, think warm, like kids hot chocolate and not uber hot like coffee when you are preparing mate'.
Haapi slurping!