I haven't built the Mill Creek, but if it doesn't address the nubs maybe that is an oversight in the manual.  I think they were spoken of in my Shearwater manual.  Anyway, those are artifacts left over from the factory cutting process - the nubs get removed.  If you DO have any locations where tab A goes into slot B, that will probably be specifically spelled out, and those tabs will be much larger and more prominent - like where bulkheads mate to hull panels.  So - sand or cut these nubs off flush with the edge line of the panel.

At the same time, even though apparently not spelled out in your manual for the edge-to-edge panel stitch joint (not lapstrake/lapstitch joints) - and I think sometimes the manuals say something about this - I think it is a best practice to bevel the edges of the panels. It can be done with a sander or sharp plane and doesn't take much time, just don't create a wavy edge on the panel. Each edge gets about 1/2 of the total angle - like a miter joint - this allows the outside edges of the panels to come together, making a very fine-line (and thus nearly invisible) joint as compared to simply stitching square-edged panels together.  This also allows the panels to stitch up better -  they don't tend to pop off towards one side or the other as you tighten stitches and try to get everything aligned.  The further from 180 degree (flat) meeting angle between panels, the more important and effective the beveling becomes. 

   And I forgot to say something very important - others have learned the lesson the very hard way - if you do bevel your panels, ber VERY carefull to ID the left/right/fore/aft orientation of the panels.  For instance, if you make a mistake and bevel two "left" panels, you create a big flaw in your boat.  A "left" beveled panel on the right side will show a great big edge of plywood veneers. I can be fixed with epoxy, filler and paint, but is not good if planning to finish bright.  If you search, you'll see others that have cried over "inadvertently erroneous beveling."  (Say that 3 times fast...)

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Nubs..............do you mean those little places where the CNC machine pauses and passes over a little piece of wood so the loose pieces don't move around on the table?    You might have some small pieces still fastened together. If that is what we're talking about I'd remove them.  

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Similar to the little connector pieces on these fillet tools? https://www.clcboats.com/shop/products/boat-building-supplies-epoxy-fiberglass-plywood/fillet-tool.html

Yep, nubs... Grumpy's asking what I was going to, shows what they come from - machining artifacts, left over from the CNC process that cuts them out - in that link.

Positioning tabs are generally longer - 3 to 4 times longer - than those leftover nubs we're discussing. Those are to be left in place as they help position components in their proper orientation during the assembly process.

Nubs should be carefully removed before dry-fitting, no later than just before final assembly, or they'll interfere with how parts are to fit.

A sharp chisel, small plane, or utility knife (box cutter to some folks) serves well, as will a sanding block or coarse file to smooth what's left after the bulk of a nub's been pared away.

   Yes thanks for all of your explanations. Seeing how they originate explains the reason they are left there but as a first time builder you question every little thing.
As for no mention in the manual I'm seeing a lot of small questions pop up that as an experienced builder are common sense but left for a newbie to figure out on their own. That's the fun part. Also through research finding alternative methods, opinions, practices etc. My guess is on your first build you'll spend an additional 20 hrs reading and rereading tips, instructions watching videos etc. ( or on the phone to CLC) I get that it all can't be put into manual, 213 pages is enough. 
 So a forum like this is has valuable as any tool in the toolbox. Thanks to all that participate, hope one day to be the one answering not asking the questions. PP

@sekodilemoseo

thanks for your input but not sure what your getting at with those links???

PP,

That's a low-life spammer who copied previous posts and added abbreviated URL links to an Indonesian gambling site. That's just the kind of bilge dirt that the "Report to Moderator" button was made for.

The exact copies of previous posts with weird or suspicious links attached is a good indicator. Another good indicator is when a thread from years back suddenly shows up with an odd generic comment that may or may not be related to the actual topic.

Pretty much all these spam posts have links in them. DO NOT CLICK ON OR FOLLOW THE LINKS! Many lead to malware or scam (or both) websites.

Laszlo

   Bubblehead, 

YES! and thanks - Bevels!!  I laid the panels out on the floor and marked with a pencil the edge(s) to get beleved.  This is poorly addressed in the manual.  I double checked myself before putting a nice 45 on every panel.

An easy way to think about bevels is to remember that those bevels will always be inside the boat.

I am no expert - so if this is incorrect; please correct my post.

Chinacoastdan

Post Script: Thanks Laszlo.  :( spammers.  I did not know what that was either.  

The spammer has been moderated. Just an FYI for anyone puzzled by that portion of this thread.

Laszlo