The magnetic flux linked with a coil is ϕ and the emf induced in it is e
Emf ε=−Ndϕdt
Where, ϕ= flux and dϕdt is the rate of flux change.
It is clear from above that emf doesn’t depend on flux, it is depend on rate of flux change.
Example : ϕ=B.Acosϕ and dϕdt=−B.Asinϕ
At 90o angle in above example flux is zero but rate of flux change is maximum.
Hence, even if ϕ is zero, emf can or cannot be zero.