The bug

Functions can skip intermediate nested functions if maxCommandChainLength (-1) commands are already queued.
While it is generally problematic when a function stops midway due to this gamerule, this specific behavior for nested functions is even more problematic:

A
>B
>C
D

Here the main function executes A, then a nested function containing B and C, and then D. Due to the behavior described above, it is possible that B and C are skipped, but D is executed. This can cause quite some problems when D relies on B and C having run before.

How to reproduce

1. Download the attached datapack MC-143269.zip and place it in the datapacks folder of your world
2. Decrease maxCommandChainLength

   /gamerule maxCommandChainLength 3
   

3. Run the function test:run_nested

   /function test:run_nested
   

   → It does not display "Nested", but it does display "Requiring nested"

Code analysis

The following is likely outdated, please also have a look at liach's patch.

See net.minecraft.advancements.FunctionManager.execute(FunctionObject, CommandSource)

This could be solved by removing the check at the beginning and always adding the nested function to the queue.
The loop removing the queue elements could also be improved by passing

maxChainCommandsCount - executedCommandsCount - 1

to the execute method of the queued command instead of maxChainCommandsCount.
With maxChainCommandsCount = MCP: i; executedCommandsCount = MCP: j
And - 1 since executedCommandsCount is incremented afterwards.

Additionally commandQueue could be changed from a ArrayDeque to a ring buffer with the size of maxCommandChainLength, created every time a non-nested function is executed. There is for example CircularFifoQueue (Apache Commons Collections) which could be used.