No, they are not saying that.
They have deemed that your current application is invalid. By this they mean that it is either incomplete or incorrect and therefore cannot be considered. You are wrong to take this to mean there is not a need for consent or that the works are permitted development.
Assuming that you own the freehold to the plot on which the garage sits and that this plot is separate (ie has diferent deeds) from the plot the house sits on then you will most likely need planning consent.
The reason they asked the question was because if it were part of the plot of the house then it's likely to achevable under PD rights of the property. But as you say it isn't, then it is unlikely that the works would be acheivable under PD rights of the [small] garage plot if it has any.
Is the garage plot attached to any other plot or was it purchased on it's own?
Given the complete lack of understanding shown above I would suggest you speak to a Professional.
There is always scope for misinterpretation.
If my posts can be interpreted in two ways, one that makes you feel angry and one that doesn't, I meant the latter.
Everyday is an opportunity to learn something new.