Graine vs. pépin
In French, 'graine' and 'pépin' both refer to seeds of plants, but they are used in different contexts and have nuanced meanings.
Graine
'Grain' refers to the seed of a plant, usually sown in the ground to grow a new plant. It is a generic term for seeds.
Je vais planter des graines de tournesol dans mon jardin.
(I am going to plant sunflower seeds in my garden.)
Les graines de chia sont très nutritives.
(Chia seeds are very nutritious.)
Tu peux acheter des graines de tomates chez le marchand.
(You can buy tomato seeds from the vendor.)
Pépin
'Pépin' specifically refers to the seed or pip of fruits, especially those found inside fruits such as apples, grapes, and oranges. It can also be used colloquially to refer to a minor inconvenience or problem.
Il ne faut pas avaler les pépins de pomme.
(You should not swallow apple seeds.)
Cette raisin a beaucoup de pépins.
(This grape has a lot of pips.)
J'ai un petit pépin avec ma voiture; elle ne démarre pas.
(I have a small problem with my car; it won't start.)
Summary
While both 'graine' and 'pépin' mean 'seed' in English, 'graine' is a general term for any kind of plant seed, and is often used when referring to planting or gardening. On the other hand, 'pépin' is used specifically for the seeds inside fruits and can also be used metaphorically to describe small problems.