Those dark splotches may be leftovers from the resin-based flux. No-clean fluxes are often made out of water-soluble resins (vs rosin) and during heating, most of it will evaporate away.
Pay attention to soldering temperatures. Sn96.5/Ag3.0/Cu0.5 solder’s liquidus is 217 °C. Soldering at high temperatures you have been using can potentially damage components, has been weakening the glue under every pad you solder (the copper is glued to the FR4), producing significantly more hazardous fumes, something that is already more hazardous with lead-free solders, and generally does nothing good.
As far as I know, it should not have a meaningful impact on the joint, but if you want to avoid this, I suggest lowering your iron temperature (and possibly getting a new tip and/or iron depending, so soldering is effective at said lower temperature), though this may not totally resolve the issue.
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