Cre-Rosa reporter labeling is a lineage tracing experiment. If the cre is expressed (even in low levels, "leaky") in a common ancestor cells during development, all the daughter cells will be labelled. In my limited experience in blood system, Ai9 tomato is very "sensitive". In other words, if your cre is expressed in low level (leaky) in earlier stage during develop, it might label cells that you do not expect. I always breed males carrying cre with females carrying Rosa reporter to avoid nonspecific recombination before and during zygote stage. However, it might still generate some random chimera during development. I had similar issue with Vav-cre (see link). We have to toss the embryos that are randomly marked. Hope this is helpful.