looks like it's just the downscaling that affects this, if set to low it's ok, medium or high causes this bug.
Good thing you found the offending setting. Now I found thid this on r169 Changelog:
There's also a new project property to control the rendering quality when downscaling (drawing sprites when they are resized smaller than their original image). This is important because the tradeoff is between quality and memory use, and in rare circumstances can also affect whether display glitches can occur due to spritesheeting. You may wish to read about how mipmaps work, since they are used to improve downscaling quality; also note we can only control mipmaps ourselves in WebGL mode - in canvas2d it's up to the browser. The three modes are:
Low quality: mipmaps are disabled (reducing memory use), but downscaling sprites can look blocky or pixellated even with linear sampling. Use this to save memory if you don't care about downscaling quality.
Medium quality: mipmaps are enabled, which adds about 1/3rd extra to the memory use, but downscaling sprites looks much better. Since the spritesheet after export is closely packed with images, in some circumstances unrelated images "bleed" together at low mipmap levels, causing display artefacts in downscaled sprites post-export.
High quality: mipmaps are enabled, but the spritesheet after export spaces and aligns images to power-of-two positions. This negates the memory saving of using a spritesheet, but guarantees that low mipmap levels never bleed separate images in to each other, ensuring glitches never appear. However there is a high cost in extra memory usage.
So I guess my question is - what triggers mipmaps? Is it C2 that does this? And if yes, then why does it trigger mipmaps when only one side is smaller than a threshold (causing terrible artifacts). I had submitted a report on this previously, but wasn't aware of which setting was responsible. Perhaps it needs some fixing so we can have best of both worlds (mip mapped when it makes sense and proper high res when it doesn't).