This is a good example of how physics is not pure math. You need to understand what the equation describes.
If you have a coil of $N$ turns with the flux through the coil changing at a constant rate, then the induced EMF caused by this is given by
$$\epsilon=\frac{\Delta \phi}{\Delta t}N$$
where $\Delta\phi$ represents the change in flux through just one turn. Therefore, we see that the more turns we have, the larger the induced EMF is. This is important. A changing magnetic flux induces an EMF.
Now, if we want to use your version of the above equation, we should take it to mean the following: If I increase the number of turns in my coil, then in order to get the same EMF I would need a smaller change in flux through one turn per unit time. Notice that I did not say your equation means that if we hold the EMF constant and then add more turns the change in flux decreases. This is because this is not a good physical picture to have, even if it true mathematically.
The problem is that you are thinking the opposite way: that the induced EMF per turn determines the change in flux. This is not the case. There is no induced magnetic flux from the EMF. You have to be careful with how you interpret your equations when you start rearranging variables.
A contrived but similar example would be to say that since $v=\frac xt$, this must mean that as time goes on, velocity always decreases. Of course this is not true. At a constant velocity the displacement also changes with time, but it just goes to show how you need to know what is physically happening. You can't just take your equation and use something that is mathematically true to determine your physical interpretation.