Can we get impurity phases due to chemical that is 99.9 percent pure since they are not 100 percent pure?
Yes purity is important parameter during chemical processes, but the value you mentioned i.e 99.9 or even 99.9999 you can consider it as pure and no need to mention the remaining 0.01 or 0.0001 as impurity phase.
Even the most standard chemical supplier can not claim for 100% pure or better to say nothing you can say as 100% pure.
You can have this link:
http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=111535981
Every chemical or material has its own set of standard, if you are getting values like 36.6% or 70% assay or purity you may mentioned it in your calculation and respective impurity phase you will get in your result.
It depends a lot for what experiment you'll be using the metals. For example in activation studies even 0.1% of impurities could play an important role. Usually suppliers of pure/hyper-pure materials give you a detailed list of the possible impurities by estimating their presence. For example see Goodfellow online catalog for some 99.9% Cu foils: http://www.goodfellow.com/catalogue/GFCat4I.php?ewd_token=5DJwmy4yXb3g2XhfnzbfrdtDrzjOp4&n=vnf7PLKFuqCtBr0gtWMKD99HzQ30Sz&ewd_urlNo=GFCat411&Catite=CU000220&CatSearNum=2
From the impurity list you can estimate the overall potential effect on the final results.
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