I can’t imagine why there would be but I think you’re only hearing mono.
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Were you using the headphones while your speaker(s) was on? If so, it could be phase cancelation from the noise canceling headphones. Even the sound of your guitar, acoustically, could create some cancelation. Just a guess. 
Is there a chance the headphone socket is a little tighter and the headphones weren’t fully inserted?
same things happens to me… barely use headphones because of it and i dont know how or why it happens. im sending my qc to get fixed on another issue but had forgotten about this. i´ll mail support and hopefully we get a fix
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I’ve played with different HP adapters, and all plug fully in.
So when I’ve experienced it, it’s’ been JUST the HP plugged into the cortex. no additional speakers.
I’ve emailed support per suggested and I’m awaiting their feedback . I’ll follow up with what they suggest
If you can barrow a set of non-noise-canceling headphones or even some wired ear buds with a 1/4" to 1/8" adaptor, that would help rule out or confirm other possible problems.
it’s a known issue, multiple threads on it unfortunately… my feeling is that is just a not very powerful headphone amp put in to this units compared to others… (some low impedance headphone seem to have it quite bad compared to others that have better results such as bayer)
this problem was prominent on any type of HP solution with low impedance i was using.
i’ve went a great deal of back and forth with support and tried a few different quad’s and the problem persists in all of them…
workarounds for me were:
-cheap desktop stereo headphone amp (problem solved)
-seems to be less prominent when i have xlr out 1 & 2 connected to my studio monitors
-higher impedance headphones ( a lot of people don’t seem to have this problem with them)
-for my case having a high MULTI OUT level(0db) and a Low HP Level (-24db) seemed to be the magic ratio to have it without doing it the annoying clipping on the spikes
I will post below their email response to both the dealer and me about this issue.
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neural reply
"We tested to put just a gain block and start raising the level. Headphones start to clip before the red light on the lane output lights up. XLR outs have more headroom and start clipping much later. With 16 ohms headphones, this can be more noticeable.
The headphones’ output has an internal gain stage of +6dB. This could explain why you feel that the signal has more headroom while using the XLR outputs. Using the Headphones level between 0dB and -3dB should be enough to avoid internal clipping. Using Quad Cortex with the Volume wheel at 100 is also safe. Please, double-check if the clipping is gone after doing this.
Notice you can boost the output blocks by accessing the LANE OUTPUT CONTROL from the grid (tap and hold the output blocks to access this menu). After that, please boost the Headphones LEVEL from the I/O Settings as much as you need and check.
Let us know how this goes!"
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TO BE CLEAR this problem is only present when using stage iem’s (usually very low impedance)
I have had this issue with a set of Audeze heaphones (LCD 4z, 15 ohm). I had to purchase a headphone amplifier to remedy the issue. Interestingly, I also have a cheap set of Superlux HD 681 headphones (32 ohm) that don’t have the issue.
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Since the Bose are noise canceling phones, the input is not connected directly to the drivers. I assume the signal feeds circuitry that mixes in the inverted-phase signal from the ambient microphones and performs their “magic processing”. No telling what kind of load it is presenting to the QC’s headphone amp. My 36 ohm ATH50s work fine. I can get a good strong signal at below 12:00 on the volume knob. I’d try another set of phones. A set of good studio phones, with more flat response would be a better choice, anyway, especially if you’ll be using them to program the QC.
Update -
I’m still working with support who has me going down the same path that you went down @Tele .
I agree with this. I have ordered a set of Beyer HP, as they will serve me better in the long run.
This exactly - Great suggestion
Lastly - (rookie mistake)… I realized that the 1/8th" > 1/4" adapter I was using was Mono… I swapped it with a stereo adapter and it did clean up the sound quite a bit. Still not perfect - but much better. I will update once my new HP’s come in.
Thank you all!
Wow, a mono 1/8" to 1/4"-don’t see those to often. Go easy on yourself, we all make rookie mistakes, even us “seasoned rookies”. 
Yes, please let us know what phones you ordered and how it works out.
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So my Beyer 770 Pro 80ohm came in today. And WOW!! What a difference. I’m seriously amazed at how clean and clear they sound. I was testing them out and found that I’d been playing over an hour -
I’ll call the problem solved. Equipment/user error’s… Not the QC
Ty
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Good news! Gotta love a happy ending. 
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Do you need to have the volume really high to hear well with those headphones? On my headphones (Sennheiser HD660S2 and AKG K701), I need my QC up at like 65 on the volume knob to head the headphones at a level I would compare to lowish levels (around 20) when listening through my speaker cab and the QC. I’ve checked the levels on the headphone output and they are nearly all the way up so it’s not that.
Hey, sorry for the delayed response - I just saw this. I really don’t. Everything is pretty balanced and not dimed. They carry volume pretty well.
Same here. My ATH50s are plenty loud at 12:00 on the volume knob. The volume of your presets will have a big impact as well.