I did not know to apply primer to my concrete before applying the semi transparent stain. Will it come up or is it safe to seal my interior floors?

Unless you are using a stain I have never seen before you do not prime concrete before staining. How to Stain Interior Concrete: 6 Steps (with Pictures) - wikiHow

Also some good suggestions here:
Behr Concrete Stain - Behr Cement Stain Tips and Reviews

Use a specialist primer to ensure that paint bonds to the smooth, hard surface: tile primer, melamine primer, or PVCu primer, as appropriate. If you have lots of small areas to prime, a multi-surface for 3 in 1 primer can be very useful. Suitable for juse on wood, metal or plaster, it will save you buying lots of separate products. For more info, just ask a professional for help.

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Originally Posted by callumj85

Use a specialist primer to ensure that paint bonds to the smooth, hard surface: tile primer, melamine primer, or PVCu primer, as appropriate. If you have lots of small areas to prime, a multi-surface for 3 in 1 primer can be very useful. Suitable for juse on wood, metal or plaster, it will save you buying lots of separate products. For more info, just ask a professional for help.

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Did you bother to read the post... He was staining a concrete driveway. Which is a very different thing.

He's staining interior concrete floors. Nevertheless, you would prime for paint but not stain. Stain is meant to seep into the material you are staining. And primer seals a surface and creates a surface paint will adhere to. If you use primer the stain will not work properly. Any decent home store or paint store can tell you what to use and how.