The main reason to that the proportion of votes went up, and the seats went down is of course that the Sweden Democrats passed the 4 % hurdle for getting parliamentary seats. With their votes now being included in the full results, the Alliance was able to raise their number of votes and lose seats.
I have some hypotheses that I would like to play around with, these are in no way based on any real data, so I have to admit that I am speculating about this, but in any case:
The red-green opposition, decided to join together to meet the alliance. This meant that the Left Party (formerly the Communist party), was guaranteed seats in the government in the case of a red-green victory. Many Social Democrats who, would refuse to vote at the Alliance therefor jumped ship and voted on the Sweden Democrats, anything to prevent Lars Ohly, the leader of the Left party from becoming a minister.
Since I am a scientist, I need to be honest and stress once again this is speculation and not based on any real "voter flow" data, but I think it is an entertaining thought anyway.
In the municipality of Täby, just north of Stockholm (a place I have a special connection to, even though I live in the Netherlands), the Moderat majority was lost. Overall the Moderates lost 11.2 % while the Liberal People Party, gained the same share. The main reason for this being local politics, and most likely being rooted with the fact that the Moderates sold of a public school (no problem with that) for virtually nothing (9.2 MSEK or roughly 1 M€) (big problem with that), the Täby council ended up in court and was found to have broken the law (sv) when selling of the public property. Despite the verdict, the council refused to do anything about it.