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The layer stacking order in 2D materials strongly affects functional properties and holds promise for next generation electronic devices. In bulk, octahedral MoTe$_2$ possesses two stacking arrangements, the Weyl semimetal T$_d$ phase, and the higher-order topological insulator 1T' phase; however, it remains unclear if thin exfoliated flakes of MoTe$_2$ follow the T$_d$, 1T', or an alternative stacking sequence. Here, we resolve this debate using atomic-resolution imaging within the transmission electron microscope. We find that the layer stacking in thin flakes of MoTe$_2$ is highly disordered and pseudo-random, which we attribute to intrinsic confinement effects. Conversely, WTe$_2$, which is isostructural and isoelectronic to MoTe$_2$, displays ordered stacking even for thin exfoliated flakes. Our results are important for understanding the quantum properties of MoTe$_2$ devices, and suggest that thickness may be used to alter the layer stacking in other 2D materials., Comment: 6 figures, 2 tables