First, make sure you are looking in the Materials tab of your Workshop and not the Crafting nor Fusion tab. Only the Materials tab will show you what your current materials are.

If you confirm that you are missing crafting materials you'll need to retrace your steps. There are only 3 ways to spend crafting materials in VEGA Conflict:

• Crafting an item in the Crafting tab
• Fusing an item in the Fusion tab
• Purchasing content in the Market/BlackMarket/Scrapyard

The last bullet point is by far the most common way players lose track of crafting materials. In order to see what materials you are spending in the various Market tabs, select the item you wish to purchase and check out its cost section. There is an expandable button that says <<FACTION>> MATERIALS (this can be ISC Materials, VSec Materials, VEGA Materials, Rebel Materials, or Demon Corps Materials). Expanding this section will show you exactly what Crafting Materials you will be spending, along with the stated gold or Blood Amber costs, in order to complete the purchase of this item.

Review any items that you have recently purchased in the Market tabs and examine their 'materials' cost. If no Crafting or Fusion was done and you are still missing Crafting Materials, then the Market is where they were spent.