Can anyone tell me the difference between pairs or couples?
Especially I need to know if you say "a pair of puffins" or "a couple of puffins" if you mean a female and male bird.
The usual term for a male and female bond is a pair not couple.
Speaking casually, "I saw a pair/couple of puffins the other day" would mean you'd seen two birds, of either sex.
As a verb, birds are said to pair, meaning male and female bonding for the purpose of rearing chicks. But to couple means to engage in sex.
In my experience pair of means 2 and couple of means 2 or more.
A pair of puffins
This would be 2 puffins.
A couple of puffins
This would be 2 or a few (small number of) puffins.
What I think you want to say is a puffin couple.
In American, we typically use the term couple to identify things that are part of a relationship but not necessarily the same.
For example My wife and I are a married couple. Just saying "They are a couple" implies that they are 2 people engaged in a romantic relationship.
Pair is usually used to describe single items with 2 parts such as a pair of scissors (with 2 blades) or a pair of pants (with 2 legs).
Where things get strange (for me at least) is that pair can also be used to describe things that are grouped because they are the same. i.e A pair of jacks.
The key here is word order and context, not word choice. If you look at the definitions of both words at dictionary.com (pair and couple), you'll find they actually use the other word in the definition. So instead of saying pair of, or couple of puffin, which could imply two non-related, you need to say a puffin pair or a puffin couple, which does imply relationship.
A couple can mean two completely different components (eg. male and female humanbeings, or two different metals, say nickel and copper) together creating a new value, for instance a family or a thermocouple, a device that measures temperature, consisting of two metals with properties no single component represents. A pair on the other hand represents two identical components: a pair of gloves, shoes, students (from the POV of their teacher they are the same)