The double quantum well systems consisting of two HgTe layers separated by a tunnel-transparent barrier are expected to manifest a variety of phase states including two-dimensional gapless semimetal and two-dimensional topological insulator. The presence of several subbands in such systems leads to a rich filling factor diagram in the quantum Hall regime. We have performed magnetotransport measurements of the HgTe-based double quantum wells in both gapless and gapped state and observed numerous crossings between the Landau levels belonging to different subbands. We analyze the Landau level crossing patterns and compare them to the results of theoretical calculations.