I don't know about all the problems. A lot could be easily explained.
Being set a year later lets a lot of flexibility. The Ore-13 could have been all used up or mined and obtained by the Decepticons. During that time the seeks could have just decided to change alt modes for one reason or another.
They are also not using facesmiles because they are now engaging attacks openly against the humans.
And when it comes to the rule being broken, it could be that they have just improved the process.