I locked my car last night using my key fob on 2011 ford mondeo estate and woke up in the morning and the fob now doesn't work I have to use the emergency key and place the key fob near the barrel and push start button few times before it recognises the key once I start driving it tells me key is out side of car I've checked related fuses and there fine any one have any idea were to look next 

Thanks 

Try changing the battery.

It 100% won't be a fuse if it works sometimes but not others. Fuses are either blown and the circuit disconnects completely, or they are intact and working.

I've changed both fobs and still nothing from the key at all the emergency system all works just struggles a little to get signal on the ignition barrel occasionally 

If you have replaced the keyfob batteries with good quality duracell CR2032 (not from Poundland) and you are still having problems then I would think it is your car battery voltage is very low. Put the battery on charge overnight.

It's a signal issue I think as it's just not receiving the signal there's no key reprogramming mode I can find as you can't put key in ignition barrel as there isn't one

 

Using a multimeter what voltage is your car battery ?