No problem, I normally clone just before flowering as I don't bother keeping mothers (yet I have about 10 -15 strains/phenos going at any time) but I've cloned at all stages. In a pinch you can clone even in flowering to save a pheno, it just takes longer because it reverts back to veg state which can take 3 weeks or so and you get some weird looking growth in that state once it roots.