1. Notice the error that you obtain:
Validate::repeated: Found indices with the same name -\[Mu].
It is telling you that you have used -mu twice. Indeed, in your definition of Lq you have (CD[-\[Mu]][\[Phi][]]) (CD[-\[Mu]][\[Phi][]]) but it should be (CD[-\[Mu]][\[Phi][]]) (CD[\[Mu]][\[Phi][]]) (one up, one down, so that they are contracted). This would solve your problem and give you the correct EOM.
2. I am not entirely sure what you mean by "but it turns out that the output is given as covariant derivative". The gradient is obtained by raising the index of the covariant derivative.