In our work, we build upon the established connection between Residual Neural Networks (ResNets) and continuous-time control systems known as NeurODEs. By construction, NeurODEs have been limited to constant-width layers, making them unsuitable for modeling deep learning architectures with width-varying layers. In this paper, we propose a continuous-time Autoencoder, which we call AutoencODE, and we extend to this case the mean-field control framework already developed for usual NeurODEs. In this setting, we tackle the case of low Tikhonov regularization, resulting in potentially non-convex cost landscapes. While the global results obtained for high Tikhonov regularization may not hold globally, we show that many of them can be recovered in regions where the loss function is locally convex. Inspired by our theoretical findings, we develop a training method tailored to this specific type of Autoencoders with residual connections, and we validate our approach through numerical experiments conducted on various examples.