Yesterday I got 3 miles to my mums then about 500 yards from her house the bike cut out, flat battery.

I looked into it today and the positive reg/rec connector had come loose in the block and was barely making contact.
It doesn't seem to like staying in there either, a slight pull on the wire will see it slide out.

I have checked the connector and the retaining pin in the block and it seems fine, it is however an aftermarket plug.

Is there any way I can make sure the positive connector stays in the block? I was thinking filling it with silicone?

It should clip in. On the spade there should be either a tab or a bump that locates inside the plug. I have a similar issue with one on mine where the heatshrink I applied over the terminal on the end of the wire interferes slightly. I used a crimper to squeeze the sides of the female side of the connector up a little tighter, and used a jeweller's screwdriver to push it fully home once the connector block was located. So far, so good.

Yeah it does clip in, but it doesn't hold it very well, it's very annoying.

I'll have to see how it holds up, might have to make the bump a little bigger with some solder or something. But silicon would work right?

Not really too sure. Normally it dries a bit flexible. Maybe a wedge of epoxy resin would do a better job if you're that worried, although I'd try nipping the connector up a bit first. If anything happens to the wire and you need to hook it out, gluing the thing in might make in impossible to salvage in the event of subsequent failure.

Its a female spade in the plug right, where the terminals bend over to form the receptacle, squeeze them tighter with soem pliers so there is more tension.

I always use switch contact compound on all my connector blocks especially the reg rec one, it won't help it stop dropping out physically but it means when its loose and possibly grinding in the hole while riding, it will help stop it sparking/burning up, its not expensive and the terminals are a lot more reliable