Cobalt pyrochlore fluoride NaCaCo$_2$F$_7$ is a disordered frustrated magnet composed of Co$^{2+}$ ions with an effective spin-$\frac{1}{2}$ magnetic moment and exhibits spin freezing below $T_f \sim$2.4 K. We perform ultrasound velocity measurements on a single crystal of the cubic NaCaCo$_2$F$_7$. The temperature dependence of the bulk modulus (the breathing elastic mode) exhibits Curie-type softening upon cooling below $\sim$20 K down to $T_f$, which is suppressed by the magnetic field... This Curie-type softening should be a precursor to the enhancement of the strength of exchange disorder via the spin-lattice coupling, which causes the spin freezing. In contrast to the magnetic-field-suppressed Curie-type softening in the bulk modulus, the trigonal shear modulus exhibits softening with a characteristic minimum upon cooling, which is enhanced by the magnetic field at temperatures below $\sim$20 K. This magnetic-field-enhanced elastic anomaly in the trigonal shear modulus suggests a coupling of the lattice to the dynamical spin-cluster state. For NaCaCo$_2$F$_7$, the observed elastic anomalies reveal an occurrence of magnetic-field-induced crossover from an isostructural lattice instability toward the spin freezing to a trigonal lattice instability arising from the emergent dynamical spin-cluster state. (read more)