The estrumate is a synthetic hormone that counteracts the corpus luteum which maintains pregnancy. This is the only thing maintaining pregnancy in cattle so is highly effective (until about 150 days in calf at which point the calf and placenta can keep pregnancy intact). In sheep and goats there are other hormones involved in maintenance of pregnancy (I shant complicate things by adding scientific names and endocrinology here) so the hormone injection is not as guaranteed. Several protocols of injecting hormone, once, more than once, with steroid, without steroid etc are listed in the literature - the more ways there are to do something in medicine, the less likely it is that any one of those ways is perfect! So it is commonly accepted that success rate of estrumate in sheep and goats is not guaranteed.
However, as the hormone acts on the mothers reproductive system, it is highly unlikely to have any adverse effect on the baby if abortion does not occur.
Hope that helps