If condensed milk and chocolate chips are, basically, your only ingredients, make sure you are using sweetened condensed milk and not just evaporated milk. The 5-minute fudge recipe has been a staple of bake sales and church socials for as long as I can remember and should work on a 3-minute microwave cycle. Some recipes mix the types of chips (milk chocolate + semi-sweet chocolate) - some recipes throw in a couple tablespoons of butter into the mix (Eagle Brand's recipe is more purist, though). But sweetened condensed milk and a LOT of chocolate chips should do the trick.
The only other problem I can think of would be if you microwaved your chips alone first and they got so hot that the chocolate seized - or if you used some kind of chocolate flavored chips that were made from mystery materials.
I don't like to use the microwave to melt chocolate - ever. For a recipe like this, I would melt the chocolate into the sweetened condensed milk over a double boiler or in a heavy saucepan over low heat - sometimes slow and steady wins the race.