Bonjour Chiara !

Thanks for your question on the site. 

I understand your confusion but here is the explanation: ''vous'' can, as you know, be used both for plural you, and for polite, formal you. 
In the second case, it has a singular meaning, as it relates to a single person.

So in le Passé Composé, when you use the formal 'vous', it will agree with the single person it refers to: it was the case here, therefore ''Vous êtes entré [...]''.

Moreover, in different contexts, you could also encounter the plural versions ''Vous êtes entrés'' or ''Vous êtes entrées'' (for a whole woman group), as well as the feminine version ''Vous êtes entrée''. 
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​I hope that's helpful.