In non-isolated, grid-tie inverter applications, it is common practice to connect the neutral point of the 3-phase AC grid to earth ground. Unfortunately, this creates a problem for DC link common mode filtering. Typical control methods utilize space vector modulation to control the power stage, which introduces a common-mode voltage in order to maximize the DC link voltage utilization. When you connect a capacitor between DC link and neutral, the space vector common-mode voltage is impressed across it. Unless the capacitor is very small, it will adversely affect operation, often leading to control loop instabilities. In addition, this capacitor will tend to resonate with the grid connect filter, causing further behavioral problems.
As such, implementing a common mode filter for these converters requires a slightly different approach in order for the system to operate correctly. First, if you are trying to control EMI, you should be able to get away with fairly small capacitors. Very low ESL is generally much more important than capacitance value. Use a number of small caps (in the range of 0.01uF) in parallel to drive ESL to an insignificant value. Even though your grid filter is inductive, the large components tend to have a lot of parasitic capacitance. Inserting a common mode inductance bypassing the three AC lines through one or more large ferrite toroids will be much more effective at mitigating high-frequency noise than the large inductors, and will reduce the EMI capacitor peak currents, and the resulting resonant frequency. Keep in mind that you are still going to see mid-frequency oscillations with this configuration, but the higher frequency EMI (several MHZ+) will be much lower.
You may also want to include a similar common mode inductor on the source side to allow common mode filtering of the supply lines. You may actually find that it’s OK for the DC link to have a moderate common-mode voltage with respect to earth ground as long as you are able to attenuate most of the common-mode signal from the AC and source lines.