How do I stop the spindle stopping when one of the axis hits the limit switch

 didn't use to happen in older versions of mach

I would think the spindle should stop when you hit the limits as that is seen as an emergency stop by Mach. I cant say if it happened or not in earlier versions but I would have thought it did. What version were you using previously? Have you possible set the spindle up in Mach where before it was manual?
Hood

but why is it an emergency if you hit a homing switch? i dont see the point

Who mentioned a Homing switch? You said a Limit.
Hood

Limit switch / homing switch pfff all the same ;-)

 I'm not sure if the table is reaching its limits or hitting the homing switch but either way the spindle stops. So is there a way to change this as its very annoying and not needed

Big difference between a limit and a home switch. If you use limits for the home switch then the difference is smaller however hitting the switch whilst NOT homing means the axis has travelled too far and is seen, as far as  Mach is concerned,  as a reason to do an E-Stop.

The easy way to solve that issue is to set up your soft limits and in that way only if something seriously goes wrong will you ever hit your Limit switches, problem solved for you

Hood

it only happens when im using the hand wheel and on the y axis, go to far and spindle stops. I was hoping there might just be a tick box or something in mach to change this

If it is only happening on the Y when using the MPG then something is not right in your setup. The limits being hit no matter which axis should put Mach into Reset and thus E-Stop.
So  if you hit X and Z limits your spindle does not stop?
Do your axes stop when hitting X an Z limits?

Hood