I don't think your input current should be going negative. If your input is indeed going negative, it would mean that you are putting power back into your source!
What kind of topology are you using? If you are using a buck converter, for example, the input current should be zero when the switching transistor is off.
What kind of compensation are you using? Buck converters are fairly easy to compensate. Boost and Buck-Boost (inverting) converters have right-hand plane zeros. As you can imagine, the small-signal models for a given topology is different depending on if you are in CCM or DCM - so your controller should be stable under both conditions. If you can post a jpeg schematic, we might be able to help.
You should also take a look at this topic **broken link removed** buck converter design issue which is somewhat related to your question.
Best regards,
\[v_c\]