My 12 week old cockapoo is doing fantastically in most respects except one....house training!

I knew it would take a little longer due to her being in the crate while I'm at work and has a pad, and the outside for when I am home, creating a little confusion.
I have religously taken her out at the key times eg after a sleep, food or when she has 'that' look about her. She will usually drop for a pee immediately and obviously I do the praise bit, I recognise the times that she usually poos so will keep her out longer and most of time she will oblige.
But....what she will often do is come back in, have a couple of minutes of play and then squat, no warning signs, and deposit poo or pee on my floor.
I never shout, but wordlessly lead her back outside, which of course she then looks at me as though I'm mad cos she's already been thanks!!
I tried getting her to use the pads and move them towards the door as she was learning, but she won't use them unless she is shut in the cage, so I gave up on that one.
Please help, as when at puppy class yesterday she was the only one who squatted inside!
Just a little info, she is a very dominant pup so I am doing all the going through doors first, making her sit for food, treats etc.