Why ADC continuous readings from software are not possible?

I have STM32F303CCTX custom board.

IO Pin PB8 has a timer that triggers a gpio high for 200us and resets for 300us. creates a 1.8KHz wave with about 35% duty using plain timer mode. Timer IRQ handler also fires the adc conversion on pin PB0.

It continuously keeps running with no values for over a minute. Then suddenly exits to second for loop with the scans(mostly invalid values).

main.c

#define ADC_ARRY_SIZE 30
 
 
uint16_t adc_vals[ADC_ARRY_SIZE] = {0};
 
uint16_t adc_val = 0;
 
uint32_t adc_zero_count = 0;
 
uint32_t index_no = 0;
 
 
void HAL_ADC_ConvCpltCallback(ADC_HandleTypeDef *hadc)
 
{
 
 adc_val = HAL_ADC_GetValue(&hadc3);
 
 if((adc_val != 0) && (index_no < ADC_ARRY_SIZE))
 
 adc_vals[index_no++] = adc_val;
 
 else if(adc_val == 0)
 
 adc_zero_count++;
 
}
 
void set_pwm2_duty(uint32_t duty_count)
 
{
 
 __HAL_TIM_SET_COMPARE(&htim2, TIM_CHANNEL_1, duty_count);
 
}
 
int main(void)
 
{
 
 adc_val = 0;
 
 adc_zero_count = 0;
 
 index_no = 0;
 
 adc_buffer_full = false;
 
 int i;
 
//Generated code begin
 
 HAL_Init();
 
 SystemClock_Config();
 
 MX_GPIO_Init();
 
 MX_ADC3_Init();
 
 MX_TIM2_Init();
 
 MX_TIM6_Init();
 
//generated code end
 
 set_laser_pwm_duty(3000);
 
 HAL_TIM_PWM_Start(&htim2, TIM_CHANNEL_1);
 
 HAL_GPIO_WritePin(GPIOB, GPIO_PIN_5, GPIO_PIN_RESET);
 
 HAL_GPIO_WritePin(GPIOGPIOB, GPIO_PIN_8, GPIO_PIN_SET);
 
 HAL_TIM_Base_Start_IT(&htim6);//start pulse timer
 
 adc_trigger = true;
 
 while (1)
 
 {
 
 /* USER CODE END WHILE */
 
 
 /* USER CODE BEGIN 3 */
 
 if(index_no >= 30)
 
 break;
 
 HAL_Delay(1);
 
 
 }
 
 HAL_TIM_Base_Stop(&htim6);//start blink timer
 
 HAL_TIM_PWM_Stop(&htim2, TIM_CHANNEL_1);
 
 HAL_ADC_Stop_IT(&hadc3);
 
 for(i=0;i<ADC_ARRY_SIZE;i++)
 
 ladc_vals[i] = adc_vals[i];
 
 for(;;);
 
}