It's a common way to tell the weather, there was an old saying of:
"Red sky in the morning, sailor's warning, red sky at night, sailor's delight."
A red tinge to cloud cover in the morning often time says that there's going to be rough weather that day, but the same tinge to the clouds in the evening says that it'll be fair weather the following day, it's not always accurate, but what Jesus was talking about there is that the signs and miracles he was doing was making it so blatantly obvious as to who he was, but they still couldn't see it, so they'd put their faith in something that wasn't always certain (like the cloud colour) but, well, we all know what they thought of Christ.
Lowering (pronounced more like Lau-er-ing) just means angry or menancing, so the sky was basically meant the weather would probably be rough and threatening.