My understanding of CPU time is that it should always be the same between every execution, on a same machine. It should require an identical amount of cpu cycles every time.
But I'm running some tests now, of executing a basic echo "Hello World", and it's giving me 0.003 to 0.005 seconds.
Is my understanding of CPU time wrong, or there's an issue in my measurement?
Your understanding is completely wrong. Real-world computers running modern OSes on modern CPUs are not simple, theoretical abstractions. There are all kinds of factors that can affect how much CPU time code requires to execute.
Consider memory bandwidth. On a typical modern machine, all the tasks running on the machine's cores are competing for access to the system memory. If the code is running at the same time code on another core is using lots of memory bandwidth, that may result in accesses to RAM taking more clock cycles.
Many other resources are shared as well, such as caches. Say the code is frequently interrupted to let other code run on the core. That will mean that the code will frequently find the cache cold and take lots of cache misses. That will also result in the code taking more clock cycles.
Let's talk about page faults as well. The code itself may be in memory or it may not be when the code starts running. Even if the code is in memory, you may or may not take soft page faults (to update the operating system's tracking of what memory is being actively used) depending on when that page last took a soft page fault or how long ago it was loaded into RAM.
And your basic hello world program is doing I/O to the terminal. The time that takes can depend on what else is interacting with the terminal at the time.