What kind of signaling protein? What kind of a mutation? Without any background, this question is not answerable. Note that the literature is full of knock-outs without obvious phenotype, so it is not unheard of that the lack of a protein does not do much.....

Paracrine signalling protein and kind of mutation is not significant.

Well, of course the kind of mutation is significant.  Without any more detailed information, one can only point out to some general aspects:

Is it a definitive null mutation or possibly not (missense)? Is it heterozygous or homozygous? If your mutation is actually only a hypomorph, you might not see the full effect.

Most paracrine signalling proteins have plenty of paralogs. Like the 22 or so FGFs. So it is always possible that other members of the family take over at least some of the function, so that you don't see an overt phenotype during development. Sometimes you will find a phenotype only when looking very closely. Different experimental systems can show different effects. Maybe your protein is actually not involved in the developmental process that you are looking at?

As I pointed out before, little to no effect of knock-outs is not at all uncommon. If you want an example of a paracrine signalling protein: Take a look at FGF1, no obvious phenotype in the knock-out mouse system. Quite often, it is unclear why (I am not really into the FGF1-literature to tell you if it is all clear in that particular case). If you have something like that, it's really your task as a scientist to come up with a hypothesis as to why and to think of experiments that can answer the question.

edit: note that I come from animal/human genetics and have no experience in plant genetics, which is what you seem to do mostly. But the principles should be similar....