It is unlikely to be due to the vagifem - mainly because, since you are already using systemic oestrogen, and also still having fairly regular natural periods, then your vaginal tissues are likely to be fairly well oestrogenised ie not fragile.
That being said, depends how you are inserting the applicator - if you've been poking it up quite firmly ( I sometimes just give it a quick shove because I'm in a hurry - I too insert mine in the morning - always when I change my patch) you might "hit" the vaginal walls and cause minor trauma which could result in spotting. I know I sometime poke mine in the wrong direction and definitely against the V walls - though it hasn't given me any spotting.
Other than that, as others said - could be your cycle breaking through it you are peri.
Spotting is much more likley to occur in post-meno women starting vagifem for the first time and who aren;t already on HRT, until the tissues have plumped up - probably the reason for your initial spotting Jules?
Hurdity x