Maybe think more about your radial when you burn apo. If you are doing anything to disturb the burn like stageing it gets tricky; trying to use an orbital stage to periapse makes timing and pitch control critical (Though you can reduce debris and wasted fuel by taking nothing unnecessary to orbit). If you are nose up after periapsis you are essentially burning a bit radial out, so you are shifting apoapsis higher but moving peri lower as well; vice versa for nose low.It's always cleaner with a high TWR stage at apo., otherwise just be very careful. P.S. I use Precise node so it's a bit easier, but not withot it's own quirks.