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As with a great many other 'violations' it will doubtless fall into the category of "you shouldn't have done that, it's contrary to P27.1, and we could take funding back" but I haven't heard of them doing so, yet. We obviously can't physically check PAYE, so there's an element of trusting that the employer has done this, therefore it'll be about demonstrating best efforts e.g., if you could evidence that you provided the employer with guidance, and that they'd committed to ensuring the apprentice was added to the same PAYE scheme, you'd probably be fine.
Apprentice & PAYE Scheme
Under the funding rules it states that an apprentice must by paid via the PAYE scheme registered on the AS, but what if it turns out they've been paid from a different PAYE scheme in error, where an employer has mutliple?