Yes this can get confusing. Every once and a while Taxonomists decide that the Latin name (or part of it), should be changed due to a new discovery of relation to other plants or a slightly different morphology etc. There are also situations where different taxonomists have names the same plant different names.
In this case Matricaria recutita, Martricaria chamomilla and Chamomilla recutita are all Latin names for the same plant, German Chamomile.
A couple more you may come across are Rosmarinus officinalis is now Salvia rosmarinus (Rosemary), Silybum marianum and Carduus marianus are both Milk Thistle.