Your oscilloscope photo indicates that you are able to measure the MCU clock at 16 MHz quite nicely.
You should be using a "10X" probe. It will add some capacitance to the MCU oscillator, which will likely shift its frequency lower. If the MCU oscillator has an input pin and an output pin, probe the output pin.
Your OWON oscilloscope has a time-base accuracy of \$\pm100\$ parts-per-million. If you need more accuracy, measure frequency with a frequency counter instead...a decent frequency counter should contain a more accurate time base.
Your OWON 'scope has an internal counter claiming 6-digit resolution. If this internal counter uses the main timebase (having accuracy of 0.01%) then its least-significant digits are suspect.
From the OWON SDS1102 manual:
It is a 6-digit single-channel counter. The counter can only measure the frequency of the triggering channel. The frequency range is from 2Hz to the full bandwidth. Only if the measured channel is in Edge mode of Single trigger type, the counter can be enabled. The counter is displayed at the bottom of the screen. Operation steps:
- 1.Push Trigger Menu button, set the trigger type to Single, set the trigger mode to Edge, select the signal source.
- 2.Push the Acquire button to show the right menu.
- 3.Select Counter as ON or OFF in the right menu.