You could list each combination as a single variation. For example, if the options are colours, instead of listing it like this

You'd list them like this

But of course, for each combination offered, you can only make available as many as the total you have (i.e. if you only have 15 red, 10 of them would be taken up by the Red & Red option, so you only have 5 left to spread between the other two options.

The other option would be to list each one in a separate listing and set up a BOGO sale, buy one get one 50% off or whatever, as that way you would be able to manage your inventory much more easily.