  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.
