Yes, there were some significant complications. Classic example - the Harecastle tunnels on the WCML were unsuitable for electrification so a 2 mile stretch of line was built on a new alignment.
As far as I can see the perceived "difficulties" we have with electrification are nothing worse than stuff we've successfully tackled previously, or that other countries have dealt with. We seem to have got into this mindset that any engineering problem we face is just far too hard, resulting in endless prevarication rather than applying ourselves and coming up with a pragmatic engineering solution. As if we've never electrified a line in a tunnel before, or a complex station throat. Is electrifying Leicester or Sheffield really that difficult, compared to say Birmingham New Street or Edinburgh Waverley?