We perform the first numerical three-dimensional studies of quantum field effects in the Bosenova experi- ment on collapsing condensates by E. Donley et al. Nature London 415, 39 2002 using the exact experimental geometry. In a stochastic truncated Wigner simulation of the collapse, the collapse times are larger than the experimentally measured values. We find that a finite temperature initial state leads to an increased creation rate of uncondensed atoms, but not to a reduction of the collapse time. A comparison of the time-dependent Hartree-Fock-Bogoliubov and Wigner methods for the more tractable spherical trap shows excellent agreement between the uncondensed populations. We conclude that the discrepancy between the experimental and theoretical values of the collapse time cannot be explained by Gaussian quantum fluctuations or finite temperature effects.