I just got through Module 1 and I’m a little confused about the plucking order differences between a couple of the lessons.
It seems on some lessons Josh goes back to the index finger at the beginning of the measure. On other lessons he will always alternate on every note plucked, even if that that means starting the measure on the middle finger.
I would stick with trying to learn to do alternating plucking for the time being. It will help you more in the long run to make that instinct right off the bat. I’d go as far as to say take it slow and be intentional about it, even if it means you progress a bit slower early on. It’s all about efficiency of motion and you’ll thank yourself later in the course.
With that said, there are plenty of times when you’ll want to play all different kinds of fingering patterns. Whether its because you’re playing whole notes so it doesn’t matter or octaves where it makes more sense to play the low note (the ones on the string closest to your face) with your index and the high note (the one closer to the bottom of the bass) with your middle finger because the middle finger tends to be longer. You’ll also have measures with mixed quarter / half / eighth notes that will have you beginning the next measure on your middle finger.
The important thing right now for you imo is to get used to alternating your plucking and mastering that.
@faydout has it right, alternate for now, it’s better to get that habit established vs having to go back later and fix it
Learning proper alternate plucking is the reason I signed up for B2B, and Josh did not disappoint.
I think the times where Josh shows a different finger pattern are really down to the number of notes and strings being played in that particular section - eg it can just make it feel more comfortable to reset your fingers or use them in a certain order.
But if it’s throwing you, as the others have said, you can stick to even alternating plucking.
Josh suggests starting with a particular finger, or repeating a particular finger within a line, because it is most ergonomic, i.e., doing so makes the line easier to play.
Sticking to straight alternate picking might seem easier because it’s what has been practiced, but everyone is best served to follow Josh’s advice regardless whether it is different from what one is used to. He is teaching, and it has a purpose.
What @MikeC says.
Every time Josh deviates from the straight always alternate pattern it is with good reason.
You might not see it at first, but it will come apparent later.
When he starts with the middle instead of the index, it usually is because somewhere in the riff there is a string change. The middle finger is longer than the index, so it is easier to make that string change from for example E string to A string with the middle finger.
The lessons are set up very well. Josh’s directions are always intentional with sound reasoning behind them. There may be alternative ways of doing things that work as well, but you will be hard pressed to find an alternative that works substantially better than what he shows.
I am fairly certain that he wants to train students into the habit of alternate plucking, but provide enough variety to not ingrain that as THE way you HAVE to do it.
He has a good video comparing different plucking-order techniques:
Thanks everyone!
Another factor sometimes when he alters the pattern is when there are repeating measures with each having an odd number of notes. If you play those strictly alternating, you’ll be starting the odd measures with your first finger and starting the even measures with your second finger. That can get confusing, especially as a beginner. So he’ll adjust the pattern so you’re playing the first note of each measure with the same finger (usually first finger), even if that means you pluck with the first finger twice in a row.
Also when there’s a rest, he’ll often start the pattern over.
As others have said, he always has good reason for doing it the way he does, even if he doesn’t say. It’s fun to try to figure out the reason. But if you can’t, don’t worry, just trust in Josh. One day after more experience you’ll come back to that passage and the reason will be obvious to you. 
Edit: Oh and if you really want to know, you can always ask him in the comments for the video, if someone else hasn’t asked already.
As a student I would just tell you to do what’s most natural and comfortable. As you begin to play more I think you’ll find yourself varying with which finger you begin a phrase and it nearly always been because it seemed easier that way.
Do work on alternating but don’t get hung up on which finger (middle or index) to start a measure with. Don’t even ask me which I do because I have no idea other than to say it probably varies. To even wonder is a distraction.
This is more helpful when playing golf and you want to get into your opponents head by asking them if they inhale or exhale as they’re standing over a crucial 3 foot putt. 
I’d like to add that we often don’t watch the right hand as beginners.
Take it really slow for a minute and just watch the plucking hand - it doesn’t matter if the left hand screws up, as long as you change to the right strings.
For example, go through a chord up and down the strings, watching your plucking fingers.
C-major starting on the A-string gives you:
When you repeat that pattern, play the last note twice, so you start on the index finger.
You can also make your own patterns, all you need to do is think about the plucking hand and take it suuuper slow. The more you drill these patterns, the easier it will be to go faster, too!
Cheers,
Antonio
Another point that comes up in later videos is that - when a specific plucking order really matters, Josh will explicitly call that out. He will directly say where using a specific finger on a specific note will matter when playing a riff at speed.