The timers run in parallel, in hardware, when you use different timer instances (e.g., TIM2, TIM3, etc.).
But the CPU that executes the interrupt service routines (aka, the functions that get triggered by the timer) does not run in parallel. So, if one takes a long time, it will block the execution of the other ISR too, or get interrupted itself (depending on interrupt priority in the NVIC).
Do you have an exact piece of code that behaves unexpectedly? Hard to say anything otherwise.