I don't think this is a Matlab compatibility issue, as much as it is a feature request.  For example, Octave and Matlab make different choices about the xlimits and ylimits for this simple code:

x = 1:10;
y = x - 6;
plot (x,y)

Matlab chooses xlimits of [1, 10] while Octave uses [0, 10].  Matlab chooses ylimits of [-5, 4] while Octave chooses [-6, 4].  This amounts to a difference of opinion, rather an incompaptibility between the two programs.  And it is simple to change the limits and ticks using various functions like ylim(), yticks(), or directly setting axes properties.

In the case of plotyy, the summary of the function is "Plot two sets of data with independent y-axes and a common x-axis."  In Octave, the y-axes really are independent and there is no code requiring that the 0-level on one axes match the 0-level on the other.

So, I'm changing the Item Group to Feature Request.  It is probably possible to write some sort of logic that decides on synchronization of number of ticks and on axes limits.

I'm lowering the Priority because there are easy workarounds.  The two axes objects are returned from plotyy() and it is simply to set ylim() and yticks() to achieve any desired synchronization of the two axes.