at first, life at animal farm seems to work perfectly. but what signs show that life is not so great? are any commandments being broken? if so, which ones and how?

Small things like certain animals being favoured and rations going disproportionally to the pigs are signs that this isn't the socialist utopia that Old Major had envisioned. The first commandments to be compromised were,

No animal shall kill any other animal (without cause)

All animals are equal (but some animals are more equal than others)