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There are many factors behind the issue.

There are many reasons behind the issue.

I am doubt about when we can use them.

What is the difference between factors and reasons?

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A factor is a situation, condition, or set of facts that contributes to, causes or strongly influences some outcome.
"Factor in" (consider) is a phrasal verb.

Studies have established that smoking is a risk factor for cancer.
A major contributing factor to the origin of a pandemic is the wild animal markets in China.
Their annual family income and family size are the crucial factors in deciding if they are eligible for welfare.
Consumer confidence in the quality of the brand is the most important factor in successful launch of a new product.
The style, condition, size and age of the property are key factors to consider when setting the sale price.
The main factors that determine the salary in a job offer are the experience and qualifications of the candidate, the range of salaries that the position commands in the marketplace, and the company salary policy.
Initial investigations show that alcohol may have been a contributing factor in the fatal accident.

A reason is an explanation for an outcome.

The reason he failed the test is because he did not prepare for it.
The student had several reasons why he chose to go to Harvard, but the principal one was the generous scholarship that they offered.