Can having a valve too short cause punctures? I recently got two punctures in two weeks on my rear wheel. I use the carrera tdf with the kenda tyres supplied. The inner tubes I used were both quite short at the valve to the point that I could only just pump it up with my hand pump. 

I would tighten the lock nut so that the valve was secure but I noticed before doing this that as pressure was released from the tube the valve would sink deeper into the rims. I was worried that this sinking effect due to decreased pressure would cause the inner tube to rip next to the valve if secured with the lock nut.

Can anyone offer an answer?
Short answer: Probably not.

Long answer: While it is technically possible to construct, a scenario, where a tube with a presta valve would get damaged,because the valve is too short/the rim is too deep, in my opinion it is highly unlikely that this is what's causing the problem. The lock nut is great to facilitate pumping your tires, but not needed once the tube is inflated. Like many other road cyclist I know, I don't even install it. I and I have never had an issue because of this. 

Generally you should look for tubes with a longer valve if you feel like the one you had was too short. AFAIK know they are available in three lengths. If you are experiencing recurring flats, you should investigate whether it always occurs in the same place and carefully examinate rim(and rim-tape coverage), and the tire. 

It's not unusual for the source of the issue(for instance a shard of glass) to be inconspicuously stuck in the tire.