Interestingly, she also speaks with a slight American accent even though we live in the Midlands.
@hugocat I don't know the country she is from in Africa and where she grew up, so this may not apply but in Nigeria, it's normal to speak with a slight American accent as American media is one of the biggest influence we have. So many children grow up learning to speak conversational English from an American pov and (British - RP) English in school, usually in more official/professional environment.
Not every single school though (especially not those in more rural areas) and not everyone speaks that way, of course. We do have our own 'posh' Nigerian English with no specific dialect (like the RP) and regular regional English dialects from different areas in Nigeria (which easily tells you the area where someone's from - like the regional dialects in England and the rest of the UK).
For some, this American/British accent can fade after a while, and not for others. So it doesn't matter that you live in the midlands.
That said, if she isn't Nigerian or from an African country where this applies as well, then please ignore.
Yes I think English is her second language, however she is clever and speaks several others.
I also have to point out this statement you made, even though I don't think you meant it as it came across (That's the point of the OP, isn't it? That people can often say something innocently, not realising how others perceive it).
I'm not sure if her being clever is a different statement altogether but adding 'however' to the fact that English is her second language before stating she's clever and speaks other languages makes it seem as though you (subconsciously) believe someone isn't clever until proven otherwise if English isn't their first language.
I do hope you know being clever or not has nothing to do with someone's first, second, third and so on language?