In The Sign of the Four, Holmes is a drug user:
Sherlock Holmes took his bottle from the corner of the mantelpiece, and his hypodermic syringe from its neat morroco case. With his long, white, nervous fingers he adjusted the delicate needle and rolled back his left shirt-cuff. For some little time his eyes rested thoughtfully upon the sinewy forearm and wrist, all dotted and scarred with innumerable puncture-marks. Finally, he thrust the sharp point home, pressed down the tiny piston, and sank back into the velvet-lined armchair with a long sigh of satisfaction.
We don't see any evidence of this addiction in A Study in Scarlet, but we do see this line:
On these occasions I have noticed such a dreamy, vacant expression in his eyes, that I might have suspected him of being addicted to the use of some narcotic, had not the temperance and cleanliness of his whole life forbidden such a notion.
This exactly describes what is happening, in-universe - he is taking drugs on those occasions. But Watson is saying that he does not see him taking the drugs, although they had been together 'many weeks'.
So - was Doyle actually writing him as taking drugs then, and Watson somehow failed to notice, or was he not (out of universe) taking them and that was a later decision?