Ah never mind my previous comments, Kriegshund has it correct. There’s a special rule just for this scenario:
“An attacking land unit can assault a coastal territory
from an ally’s transport, but only on the turn of
the attacking land unit’s owner. All of the normal
requirements for transports offloading in a sea
zone must still be met by the attacking power (see
“Special Combat Movement, Transports”, page 16),
and any scrambled air units will prevent the landing
if they cannot be destroyed”
http://media.wizards.com/2015/downloads/ah/AA_europe_1940_rules.pdf (page 21)
On page 16 it permits a scramble to resist amphibious attacks:
“They can also be scrambled to resist amphibious
assaults from adjacent sea zones”
