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But if that's the cause then often a quick exit and reload will do the trick.... you will find sometimes things like the tree or plant spreaders didn't load or some such too, such things all seem to be related little 'oops' that happen on occasion. Less commonly that when in EA, but it does sometimes still happen, just much more rarely now.
Oh, and, I almost forgot to mention, even if you still can't pick them up, try deconstructing them, at least that way you can get back the materials and clear the obstacles...
Flares are a great source of components btw, so it may be worth deconstructing any excess you get from portals in the recycler (but you can light them and deconstruct them manually too which might actually be faster if you have a bundle and drop them outside since the recycler is so clunky to use).
Sorry to hear that the exit/reload didn't help. Ah well. Sometimes you have to move around a little, back and forth and such, to get the durn things to highlight so you can deconstruct them... if you can't get them to highlight there might be a clipping problem, in which case the only way out I know of involves editing the save file, which I've not been quite brave enough to attempt... yet, at least! Maybe somebody else will chime in, or you can search the comments, it's been discussed a fair bit....
If you drop them you can pick them up, but if you right-click them you have to deconstruct them to get the materials back - either that or trigger the thing...