Hidden trackable information in games sucks!
I play games for fun and pursuing the goal to win the game is fun! :)
The icon on the wonder does not use the brown/grey circle in the icon, so it should count every stone you produce from any source. So the yellow cards should be included.
I agree that it *should* - not only because of the iconography which indeed doesn't include any brown, but primarily because Stonehenge is quite clearly the weakest wonder otherwise and is in bad need of making it stronger.
However, the official rules explicitly say otherwise in the rulesheet for the Wonder Pack, they say to only count the "Stone resource symbol(s) present on the player’s brown cards". (This is not a translation problem, it is in the French original as well.)
So counting the Stone symbol on the yellow Caravansery is a house rule, albeit one that I find very sensible and use myself - although I am not too fond of house rules in general and only use one when I deem it really necessary.
It has already been mentioned as a variant here.
A further question when using this house rule with Cities and Leaders is how to treat Stones produced with the black cards Secret Warehouse and Black Market (although the latter is rarely relevant) and the leader Bilkis.
I tend to think that all of them should count in order to make Stonehenge stronger, both sides really need it.
So for now I play with the house rule that you score for the maximum number of Stones you can produce in a turn *without your neighbours*. (And that you don't need to pay a coin for Bilkis when counting her.)