We present experimental and numerical results for the parametric fluctuation properties in the spectra of classically chaotic quantum graphs with unitary or symplectic symmetry. A level dynamics is realized by changing the lengths of a few bonds parametrically. The long-range correlations in the spectra reveal at a fixed parameter value deviations from those expected for generic chaotic systems with corresponding universality class. They originate from modes which are confined to individual bonds or explore only a fraction of the quantum graph. Similarly, discrepancies are observed in the avoided-crossing distribution, velocity correlation function, and the curvature distribution of the level dynamics which also may be attributed to such localized modes. We demonstrate that these may be easily identified by inspecting the level dynamics and consequently their nonuniversal contributions to the parametric spectral properties may be diminished considerably. This is corroborated by numerical studies.