With the information you presented, I've re-visited the Logo and experimented with the various blend modes and arrived at the blend modes that seem acceptable to me. I was using Transparency settings to control the color, instead of shade as I was probably supposed to use all along.
The anomalies, as they appeared originally began when I made the decision to edit the letter corners from squared off to sharper points. The original letter started as a Text frame that I converted to a polygon frame and was Combined last in the process with the cartouche shape. The cartouche was in itself an earlier set of four combined polygons using The Path Operations:
The first was combining the two separately created capsules or pills into a single ring shape (I couldn't do this well using Transform, the circles transformed but skewed the sides). The ring at this point stood as it's own shape with the lighter gold color no internal fill (the strong yellow).
The second was combining the "knot" or "rope braid" polygon (created using Duplicate) over the ring using Path Operators.
The third was combining the the ring/knot over the bar using Path Operations to create the finished cartouche, now a stand alone single polygon.
The fourth was combining the letter (converted to a polygon shape) over the cartouche using Path Operators.
All was happy at this point, but then I decided to edit the letter shape, which at that point was part of the entire combined polygon. In a tutorial on Editing Shapes it was advised not to use "Undo" combined polygons as the results are not predictable, thus I used Item > Split Polygons, but I wonder if a lot more went on behind the scenes. When I clicked Split command; bingo, the deep yellow fill appeared into the center of the light gold cartouche with no further action. I left that as is for the moment because the letter and the cartouche both had their own separate frames returned. I did note that the Split Polygons option was unavailable to earlier combinations beyond the last two.
Double clicking on the letter polygon to activate the Node dialog box, I was able the sharpen the bottom and the serif tops of the letter and move the letter up a little relative to the cartouche. That is when I noted that the (cyan) letter had left it's unedited ghost inside the letter frame but colored the same as the light gold cartouche, not the cyan, and remained largely un-amendable.
Since then I have noted a couple of things about the letter's ghost: The light gold indicates that it had de-coupled itself from the letter and attached itself as part of the cartouche, also that the ghost had subsumed itself into the cartouche as an indistinguishable shape--the letter overlaid (and overlays) the cartouche. Note just below where the letter crosses over the cartouche.
I have been able to edit portions of the ghost (see enclosed new zip file and by the way OS X 10.11.6). I can select the letter's shape frame and double click to enter the letter's and ghost's Node structure. However only the portion of the ghost that originally laid outside the cartouche. You will see that here the ghost's Nodes have been edited to conform to the outline of the letter; in other words the ghost has been tucked into the letter until both are the same. Voila, the ghost disappears. The portion of the letter's ghost that lies inside the cartouche remains unselectable and uneditable even though it is part of the letter's shape frame and the letter itself is editable. Also the potion of the ghost that is uneditable overlies the deep yellow.
Also I noted that the two Split Polygons are not the letter's polygon frame and the final cartouche's polygon frame, but the letter's frame and the cartouche's frame that has expanded to include the letter's separate frame as well.
For some reason hashing around with this, I thought I would see what happens on export to a PDF. I was immediately presented with PreFlight Verifier telling me that three (not two) polygons have transparencies, even though opacity is now set at 100%(?). There should have been only two split polygons at this point. I queried the third one and it gave me a--let me call it a ghost frame--that included only the first capsule created at the beginning of the cartouche and long ago subsumed via Combine Polygons into the finished cartouche in the first step (see above). Also this capsule is the one filled with the sudden and belated appearance of the deep yellow. As a clue, I note this one is called "Polygon 3", which might refer to that first Combined Polygon created. I don't think I used the Path Operators then, just the Combine command.
This third polygon can be selected only through selecting it from the Preflight Verifier and is uneditable, no Nodes can be attached to it and it cannot be recognized any other way. Otherwise it remains invisible. Also within this "Polygon 3" is the un-amendable portion of the letter's ghost. A ghost within a ghost.
I have blown the logo down to as low 5/8" (9.5 mm), including the unfinished text frame at the bottom, and printed it in greyscale. Baring the letter's ghost, the deep yellow is quite striking in greyscale and now I want to keep it. Happy accident. The only ill effect is still the letter's ghost, which at that size causes the serifs to blur, become fuzzy.
From all that I have given above in the way of history for this, can you see a path that will allow me to activate this interior portion of the letter's ghost and edit it out? If you can that would be appreciated. If not, I hope all this will be of help to others.
Also for a test, I clicked Ignore Errors (transparencies) in Preflight Verifier and exported the logo to PDF. It did not give me the option to export as, the required, PDF-x-1a. Do you see a reason why this PDF/X type was not an option? I do note that layers and transparencies can be issues, but now there are now no transparencies(?) and only one layer, yet the Preflight Verifier still registers the message.
One more question for the future. Finally I want to edit and convert the text frame to a polygon and Combine Polygons with the cartouche/letter polygon for a single logo polygon. This is a case where there is no physical connection between the two combined parts. Is this likely to be a known problem?