I thought it was pretty obvious that Gerry McCann was speaking "with hindsight" - that having gone over and over things in his mind, he realised that the abductor could have been in the flat when he checked at 9.30.
The way it's being interpreted by some is as though he has just suddenly decided to say that when he checked on the kids he thought (at that time) that someone was in the flat.
Years ago, I came home from having spent the day helping friends to move into their new house. My dog seemed subdued and when I opened the door to let her out, she sniffed outside the door but didn't want to go out. She was very old and I thought she was being fussy, so I made her go out and I merrily went about my business preparing dinner. Over the next hour, I answered a couple of telephone calls and made dinner and then my husband came home with our children whom he'd picked up from a friend's. A moment or so after he came in the front door, he called to me "Hey, what have you done with the television?" My first instinct was that the settings on the tv must be wrong and I was thinking 'powercut' but I replied "Why? What's wrong with the television?" My husband replied "It's gone". And sure enough, we'd been burgled. They'd taken the tv, two video recorders, money, jewellery, a camera, clothes... Our bedroom had been ransacked. I hadn't noticed because when I'd come home, I'd gone straight into the kitchen and had only emerged to answer a couple of phone calls in the hall.
It was only later that I recalled the dog's behaviour and that it made some sense to me. We discovered that the burglar had entered and probably left too by the patio door in the dining room next door to the kitchen. The dog was probably sniffing the air because she could still smell him. The police also thought I'd disturbed him because he took two of my husband's suits and we found them discarded in a lane behind the house. The police said that he probably grabbed them and ran with a view to going through the pockets when he was clear of the house.
I think if Gerry had thought at the time that there was someone in the flat, he wouldn't have just gone off back to the others in the restaurant.