We investigate simulation-based bandpower covariance matrices commonly used in cosmological parameter inferences such as the estimation of the tensor-to-scalar ratio 𝑟. We find that upper limits on 𝑟 can be biased low. The underestimation of the upper limit is most severe when the number of simulation realizations is similar to the number of observables. Convergence of the covariance-matrix estimation can require a number of simulations an order of magnitude larger than the number of observables. This is found to be caused by an additional scatter in the posterior probability of 𝑟 due to Monte Carlo noise in the estimated bandpower covariance matrix, in particular, by spurious non-zero off-diagonal elements. We show that matrix conditioning can be a viable mitigation strategy in the case that legitimate covariance assumptions can be made.