Whenever I destroy a trap, parts or synthites clip through objects.
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I just saw this blinking but my timing was a bit off so my screenshot doesn't show it but I put a yellow circle where it's exactly located. Look at bottom left on my next screenshot down below and you'll see that I obtained Synthite highlighted by a red circle.
So basically the Synthite that I collected was clipping through the floor and ended up sitting in the ceiling for which I jumped and collected it but it's easy to miss if you're not paying attention. Most resources are ending up missing without us noticing.