每隔 means "every". It can be used as "每隔" + quantity + unit.
- every + 2 + days = 每隔+两(2)+天
I drink a cup of coffee every two days. = 我每隔2天喝一杯咖啡。
This means you consume a cup of coffee every 48 hour interval.
- every 500 meters = 每隔 + 五百(500) + 米
I stop every 500 meters. = 我每隔500米停一次。
It means you stop at 500 meters, and stop again when you reach 1000 meters.
In conclusion, as my understanding, "每隔两天" means "every 2 days"(not 3).
However, your concern is legit. It is a vague way of saying things. Thus, if it is a more serious situation (e.g. contract), instead of a day to day conversation, you should clarify.