How do we reconcile the different definitions for 弊端 in the HSK Standard Course 6上 ("disadvantage" etc.) and CC-CEDICT ("malpractice" etc.)?
I suggest we have a look at some Chinese dictionaries.
现代汉语规范词典 (GF) has this:
弊端
bìduān 
名 由于制度上或工作中的漏洞而引发的有害的事情
管理不严酿成弊端。

I don't find this particularly helpful. Whereas 现代汉语大词典 (XHD) has this:
弊端
bì duān 
1 弊病产生的原因。如：消除弊端。
2 弊病。如：种种弊端, 不胜枚举。

My TL;DR translation is: &quot;that which causes 弊病; 弊病&quot; (omitting the sample sentences which again aren't so helpful here). So this definition is based around 弊病. From this we can fairly safely say that 弊病 and 弊端 have similar meanings and are near-synonyms (近义词). It turns out that CC-CEDICT has this for 弊病:
弊病
bìbìng
1 malady
2 evil
3 malpractice
4 drawback
5 disadvantage

And so we have both meanings: drawback/disadvantage, and malpractice.
My conclusion is that here we have some 弊端/shortcomings in both the HSK 6 definitions and in CC-CEDICT.
It seems that 弊端 is poorly translated in general. The only Western dictionary I have on my Pleco that has both of these meanings is CC-CFDICT (Chinese to French).
Edit (2021-03-27): The CC-CEDICT definition has been updated. The new definition is simply: &quot;systemic problem (sometimes refers specifically to corrupt practices)&quot;. The CC-CEDICT  editor gave some interesting analysis in the change log for the updated CC-CEDICT definition, and commented: &quot;
I think our current definition was probably adequate for the way 弊端 was used 50 or 60 years ago, but the meaning has evidently become broader over recent decades, and dictionaries haven't kept up with the change.&quot;