Molecular beam epitaxy is a deposition technique providing high-quality single-crystalline samples with extremely high carrier mobility and very sharp heterointerfaces. It is often used to produce very specific devices like high-mobility transistors, high-detectivity infrared photodetectors, and high-efficiency solar cells, which may eventually contain quantum dots. As a consequence, optimization of the optical properties of such nanostructures is very important as it can improve device performance. Here, we compare photoluminescence data of samples containing InAs quantum dots covered by a thin GaAs layer which was deposited either by conventional molecular beam epitaxy or by an alternative method called migration enhanced epitaxy. We show that the latter provides better samples but also enhances indium segregation. We provide a consistent explanation of the data and discuss ways to improve the growth conditions and get better results.