Joseph also found a pair of men's underwear that smelled of bleach under her daughter's bed, the complaint said.
Personal belongings were missing from Alexandria's dresser and closets, and the bed was stripped of all sheets, comforters and pillows, officials said.
Blood splatter was found in Alexandria's bedroom, on the foot of an oversized stuffed animal, in the hallway and in a bathroom, the complaint said.
Orange County Sheriff Jerry Demings on Wednesday called the disappearance of the Olympia High student "extremely suspicious."
And her mother's longtime live-in boyfriend, Sanel Saint Simon, 43, is now in custody, deputies said.
Saint Simon has been charged with providing false information to a law-enforcement officer and attempted destruction of evidence.
Authorities allege that Saint Simon tried to clean up the blood with bleach, Demings said.
Saint Simon also has been "untruthful" in much of what he told investigators, Demings said.
Officials are seeking information about Saint Simon's whereabouts from 10 a.m. to 3 p.m. Monday. Saint Simon went to work at Boston Market on South Kirkman Road around 7 a.m. but left without clocking out around 9:30 a.m., according to the complaint. Saint Simon originally told investigators he was at work all day but later recanted and said he was at a nearby shopping plaza.
Officials said Saint Simon was possibly driving a black Pontiac. The vehicle, which belongs to Saint Simon's uncle, was recovered along Silver Star Road in Pine Hills and is being processed, Demings said. His uncle told police that Saint Simon asked him not to tell police that he was in possession of his Pontiac, according to the criminal complaint.
Saint Simon is at the Orange County Jail on a $7,650 bond. During his first appearance in court Wednesday afternoon, he needed an interpreter who spoke Creole.
According to a Florida Department of Law Enforcement report, Saint Simon does not have a previous criminal record.
"Saint Simon's lack of truthfulness about his actions on the day Alexandria went missing has raised our suspicions about Alexandria's well-being," said Demings. "If anyone knows where Alexandria is, let us know. It is critical that we find out that she is OK, since indications are she may be in need of our help."
The Sheriff's Office said there is concern for Alexandria's well-being because it is unusual for her to not contact her family, she can't be reached on her cellphone, she hasn't updated her social-media accounts and she does not have a history of running away.
Alexandria's friends have taken to social media to help spread the word about the teen's disappearance.
Thousands are using the hashtag #BringAlexHome in Facebook posts, tweets and Instagram photos.
Alexandria's friends have also announced on social media a "March for Alex" at 2 p.m. Thursday. Participants are asked to meet at the Publix near Good Homes Road and wear pink or white.
Alexandria has black hair, brown eyes, weighs 105 pounds and is 5-feet-2. It is unknown what she was wearing.
Anyone with information about Alexandria's whereabouts is asked to call the Sheriff's Office at 407-836-4357.