There ought to be yellow readers at East India Station. They are probably at street level. There are no gates at virtually all DLR stations.
You don’t need to touch any readers while changing at Canning Town.
You will have been charged for an incomplete journey which is £8.90 at peak times. You may be able to correct this online if your card is registered to a TfL account. Otherwise you can call the helpdesk and explain what happened.