I'm not sure what you mean so I'll explain two different scenarios.
1. Cloning a plant thats flowering during the flowering cycle can lead to some messed up clones. Some people know how to revert plants back into vegging and it works with some success. Generally though, if your a novice to such a technique nothing but bad consequences can come from it.
2. If you meant is it okay to clone a vegging plant in a flowering room...then no you can't...for the clones to root they'll need 18 to 24 hours of light to develop roots properly (so basically you should use a vegging room or it will take a long while to get roots or they just won't develop properly). If you put rooted clones in a flowering room then they will flower into little plants ALA SOG. Little plants flower the same way big plants do. If you put clones that have roots in a flower room (12/12 lighting) then they'll flower just like any other plant would. They'll basically skip most of the vegging process (generally they veg for a week or 2 even in 12/12 lighting).
Basically if you want to grow full sized plants then veg the clones in a vegging room and grow them out to your desired hight. If you want a lot of little fruiting plants then vegg the clones out for a week or two till they have roots and then place them in the flowering area. Bottomline is you'll need somewhere to veg your plants even temporarily till they have roots.