You first need to ask yourself what is the point for you of probation periods and what do you get out of them. I won't rehearse the arguments over them having no basis in statute but merely being a vehicle for management but if you do a search you will find lots of debate. What do you do differently during a probation period (and why) than you don't after the end of it but before two years service is completed? Is this helpful to the employer? The manager?

I would generally say that if you are going to use probation periods in a school environment then (if you have control over T&Cs) as far as possible I would link it to terms not months and have it always finishing at end of a term.

On your specific issue I do not believe that there can be a successful challenge against your practice (to do it at the end of a term rather than in holidays) as whilst it may seem unfair its not unfair for a reason protected by law.

Hi Gemma, it depends whether you are following national terms and conditions or if you have consulted to move away from these.
Under national terms and conditions, teachers are deemed to have passed probation once they have completed their NQT year.
Are you in a MAT? It is unlikely that you have derecognised your Unions, in which case you will still be bound by these terms and conditions. While you can use different terms (including a probation period) on new starters, it is likely to provide unintended consequences like the ones you describe above.
Do you have an active JCC? I would suggest doing some more digging into where these probation periods come from. I would also be expecting some kickback if this moves towards dismissal.
Probation tends to be used infrequently and poorly in schools, even for support staff.