1.The girl has a great interest in sport and has been taking badminton classes twice a week over the last three years.

这个句子时态正确。has a great interest为静态动词表示长期状态，该状态在说话时存在着，就用一般现在时。has been taking badminton classes twice a week为一个临时习惯从过去持续到说话时，所以用现在完成进行时。如果是长期习惯，则用现在完成时+持续时间状语。一个人一周二次去羽毛球训练班练球是一个预料会结束的临时习惯。临时习惯持续至今要用现在完成进行时。长期习惯（不可预料结束的习惯）持续至今要用现在完成时+持续时间状语。例如：He has written to parents twice a month for the past 10 years.

2.We had been best friends since primary school and spend almost every day with each other. （错误）

这个句子时态错误。要么将had been改为has been, 要么将spend改为spent。

We has been best friends since primary school and spend almost every day with each other. (正确）

We had been best friends since primary school and spent almost every day with each other. （正确）