Usage of 'should have'

"Should have" can also refer to something you were assumed to do, without specifying whether you did it or not.

How much did I spend on movies last year? Well, a movie costs about $10, and I went to a movie about once a month, so I should have spent about $120.

In this example, it does not mean spending money was a good idea, and it does not mean I didn't do it.

The following is the sense of should that's being used in the article:

[Merriam-Webster]
4 —used in auxiliary function to express what is probable or expected
    // with an early start, they should be here by noon

The following is a paraphrase of this sense, as used in the article:

It is likely [they were] part of the scheme for two years during the period from April 1, 2018, to March 31, 2020, and it is likely [they] contributed at least for 78 days from October 1, 2019, to March 31, 2020 and also in one of the other three six monthly contribution periods from April 1, 2018.