"¿Cuándo estuviste en ese barco?"

Why? " Stayed" is given as an alternative for estuviste. Does it just mean " you were" and in which case why should "stayed " be given as an alternative?

I'd like to know this as well, since it says that "estuve" could mean "stayed."

Not usually. Being "at" a boat is like being in the same location as the boat, but not in or on it. If you are standing next to a boat, then yes, you are at the boat. However, if you are walking on the deck of the boat, you are either in or on it.

'Estuviste' is the 'tú' form conjugation of 'estar' in the preterite. There is nothing ambiguous about it.

Just like any other verb and tense, estar has different forms for each person and number in the preterite tense. They are as follows:

Yo estuve / Nosotros estuvimos

Tú estuviste / Vosotros estuvisteis

Él estuvo / Ellos estuvieron