Freedom of movement (and a lot of other things) is guaranteed in the Bilateral I agreements [0] between the EU and Switzerland which are protected by a so-called guillotine clause [1]. The latter meaning that violation of any part of the agreement would void all of it.

The result of the referendum would definitely violate part of the agreement and the EU just reminded Switzerland of the consequences.

If anything it could be blamed on the initiators and supporters (SVP) of the referendum to not properly inform the populace of the consequences of a successful referendum.

[0] https://en.wikipedia.org/wiki/Switzerland%E2%80%93European_U...

[1] https://en.wikipedia.org/wiki/Guillotine_clause