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I've recently been looking I to the trygon branch of the tyranid race and was wondering what are the main differences between a trygon and a prime? In all aspects from the fluff and are there any physical differences between the two model wise?

Also why do some of the trygons remain as just trygons and some become primes? What is the benefit for the hive mind to have the two different sub species?

Well, the Prime is synapse and the other isn't. The Hive Mind decides that if they need synapse for the tunnelling nids like ravenors or tunnelling ripper swarms the Hive Mind will use Primes. But if there is enough synapse already, the Mind will use normal Trygons.

So far as physical differences, the plastic kit comes with an alternative head and a couple other bits to help distinguish a Prime from a regular Trygon.

There's also plenty of creatures that get more 'senior' variants, Warror Primes, the Swarmlord, and certain fluff has mentioned Alpha Lictors before. Some of the more complex Tyranids do get more individuality despite still being bound to the hive mind.

Basically the head and frontal plates on the Prime are spikey, where the normal Trygon is smooth, and the Prime has over-sized mandibles.