Do Ligands electrons fill the d-orbitals of the metal ion?
You are mistaken. The electron pairs donated in the coordinate bonds by the ligands do not fill the d orbitals of the metal ion.

The basis of crystal field theory is the electrostatic repulsion between the d orbitals of the central metal ion and the electron cloud of the ligands. This repulsion then leads to the breaking of the degeneracy of the orbitals, giving rise to disparity in energy between different sets of d orbitals. This arises due to the different spatial orientations of the 5 d orbitals (i.e. $xy, yz, xz, x^2-y^2, z^2$). Thus, they experience different amounts of repulsion from the ligands when the ligands are oriented in different geometric configurations (i.e. octahedral, square planar, tetrahedral etc.) around the central metal ion.

For more details on crystal field theory and an alternative explanation known as ligand field theory (based on molecular orbital theory), you can refer to the following discussion:

In an octahedral complex, what happens to the electrons donated by the ligand?

Since the d orbitals are not filled up by any ligand electrons, the electronic transitions between the orbitals of different energy levels (such as in the case of $t2g$ and $eg*$) are certainly possible. 

Now, you may wonder: Where do the donated electrons go? 

Well... based on valence bond theory, they are used in the formation of covalent bonds between the central metal ion and the ligands. These covalent bonding interactions are described as the overlap of the ligands' atomic orbitals with the electron pairs with the hybrid atomic orbitals of the central metal ion. 

For example, in the case of a hexaaquairon (III) complex, the iron (III) ion has 5 electrons, each singly occupying one d orbital. As the d orbitals are occupied, the vacant 4s, 4p and 4d orbitals are hybridised to give 6 $sp^3d^2$ orbitals to be used to overlap with the atomic orbitals of the ligands. 

Thus, the donated electrons actually are "shared" between the valence atomic orbitals of the ligand and the valence hybrid orbitals of the metal ion. 

Hope I have clarified your doubts.