Development tools for Zephyr on STM32Workbench for Zephyr: VS Code extension to set up, build, flash and debug Zephyr applications on STM32.Devicetree manager: browse, edit and visualize Zephyr devicetree, STM32CubeMX-like for Zephyr.
Unfortunately we cannot not reproduce the issue.
So could please attach an the *.ioc, stm32f3xx_hal_timebase_TIM.c and stm32f3xx_it.c to investigate the problem.