Hi,
This warning message usually pops up when dealing with a resonant structure. You can trust the results up to a certain extent. For example, if you are interested in S-parameters, it is ok to determine the resonance frequency. Also, take a look at the time signal, if most of the energy has vanished and all the rest is just oscilating then you can be sure this warning is due to resonance.
How to deal with it?
There are many ways that I can think of, but if I assume that your structure is a resonating one, as a first step, I'd try to increase the "number of pulses" in the transient special settings.
Good luck,
P.