Board meeting in case of small companies

It is not like that. 

Act is giving some privileges/exemptions to a small company. One of which is A small company may hold only two board meetings in a year, i.e. one Board Meeting in each half of the calender year with a minimum gap of ninety days between the two meetings.

A small company may hold more than 2 meetings.  However if only two meetings are held in a year, above timeline should be adhered. Act is not prohibiting small company from holding more than 2 meetings.