I have a 2006 ford Fiesta with the semi-automatic (Durashift EST)  it won’t start and says transmission malfunction but I tried to start it for the first time a day later, there was no 'transmission malfunction.' The car started and drove perfectly in all gears, including automatic and reverse. I drove it for an hour, stopping and restarting, and everything was fine.

However, two days later, I attempted to start the car again and encountered the same original problem

Fully charge the battery or replace the battery if you don't know when it was last changed

Lubricate the clutch actuator and gear shift mechanisms

I got a new battery put in yday was hoping it was that but the same thing happened again started up drove fine for a few hours switching engine off went shopping was okay after that started up drove fine went home drop stuff off went straight back out but came up again with transmission malfunction 

You're going to need to set yourself up on FORScan then and read the codes.

Iv just tried the car again it’s starting and driving fine again but no doubt will happen again Okay I’m gonna take it into a garage to get full diagnostics I just hope it’s not an expensive repair 

Try lubricating the mechanisms, as suggested, they could be stiff

Remember, it's just a conventional manual gearbox and clutch but with robotised clutch operation, throttle and gear change operation

I would suggest FORScan, read the codes, see what is happening.

Before you let a garage loose on it

It says on it cylinder 3 misfire 

9 hours ago, Kierman said:

It says on it cylinder 3 misfire 

There you go then, that's probably not helping, it needs full throttle response to change gears and a misfire isn't giving you full throttle response

Sweet I had a look online and could coils and spark plugs cos it’s sending the wrong rpm so it’s putting the car in fail safe mode saying transmission malfunction 

You need to diagnose and fix the issues properly, not guess.

If it's misfiring it's usually plugs or HT leads or coil pack, yes,  so I would change all three items with genuine new, NOT cheap Chinese copies

It just seems to me that the car just needs full good service, something that it obviously hasn't had for a very long time