Annotations that are candidates for removal:
1) CG1162 shows no evidence of coding in that I do not see any wobble upon EvoPrinting.
2) EvoPrinting CG31179 yields no trace of a wobble, and I doubt whether it is a gene. There are a couple ESTs but these do not coincide well with the transcript.
Evidence of ORFs in currently annotated UTRs:
1) In EvoPrinting Trl, I found indication of coding sequence in the 3'UTR.  There is an ORF in this
sequence. 
2) The following sequence is in the 3'UTR of dan, but exhibits a wobble signature, as indicated by the EvoPrint given below.  There are no stops in the sequence.  Since dan is in the intron of another gene it could belong to that other gene.
GAaAAGCCaAAGTTGGCgCCcacGGAGCCAGCCACGGATAcagagatagaggatagcccagacggtgctctgcacg
atgcagagccaggacccggtgtcctggctacagatgcaaatgcagataccgccgagggctcgacgaggtgccatgt
ctatgcgccggccgtctaccgatcgtcgGCcACcCTaCTCAGCTCcCTGTTCTTCCCtCCCTACGAATTTGTACAt
TGTGACCTCGAcGAtGACCCcGAcGAcTGCCAgATcACGGGCGAGTAcCAGCAGTaCGAcGAAcTgAgcTCcAGCA
G
3) In the undefined 3'UTR of Octbeta2R a wobble signature recognized by EvoPrinter
aacattacgagtaaatcagccgacgcatttgccgGCATATTAATTTTacAAATTAATGGAacac
ttTaATTGCATTaaATtGAttccacccatccggctggcatcgattgattcgattcgcatccttacaccagtcgca
ccatttgcaccatttgcaccatttACACaTGaCTcgaggccgtcGAGGCgGCggcaTTGTTgTTcTTgTTCCATT
TGTTGATgTACTCCATGGGTATtTCaATcTGgATCTCCTGCACATCgTCgcccgccaagcaatcgacattggatt
tgcccttgcccgcatccttgcccgtatcctttgcatccttcgactccctgccatccttggcggcagctgccaatt
gtccgcccaggcgggatccgccCGCCGCCAGCCGCTGCTGCTGCTGgGCgatggGgGTCAGcAGCGCCTCaTCCC
TGTA
Other corrections:
1) I have found a potential ORF in an intron <up>of sv</up>.  Every non-conserved base in the EvoPrint, given below, fits in with wobble.  It could be a short functional peptide.  You might look and see if there is other evidence for it.
ATGGAcCTaTCTACAGCaTAtCGCTACAAcCAgAAcATGATGGAATAcTAcACATGTAA
2) Dif is annotated incorrectly at UCSC, and a blast of a solid ORF yields no ORF in FlyBase BLAST.  I attach the EvoPrint.  The ORF is in the reverse directions.
gaaaatatctcgttatcccattttgtcttcaaatcagttatccgtaacccaattcatctactccaAgCCa
tTtGcCTCcGCcAgccgcCgtGCtATtTCAtccGcactcaaaaaatcggtcgtatccactccaccagttgctgct
ccaccttcgccgcactccccgccaaatggtggtTCcGGaCttTTGCTGGTgTAcAaaGCAAAGTGtTCcGCcTCG
GAgAGaTCCACaCTGGGATCcagcacaacACCaTAGGCtCCCTCGCAcAgATTCTTGATGCTCTGcctgtcgGCg
ATGGCaAtCAatTCCATaTTGCCgTCaCTtATGGGaATATCcGCCAgtTGcAGaGTGCTCAGGGTCTTcCtaTCc
AGcGGTCGaCCgTAaCTaAGGGTGCTGGCATTcGAGTAGCTCTCcGGtCgtAGCAaaCTGTTCTCGCTaTCGCCt
CCCTTCAatGGTATGTGaATaACATCcGCaTCCAGgTgGGCaGGtCttTTaCCCGAtACaCTGCTcGAaCTaCGA
CcgactggcttgccatttcgaccctcactttttcccagtggCTGCAtcgatcttgtgGAGCtgCGaTTGGGATCt
cCCAGgGaaAAGTGcgcaacgcttggttccctactgccggtgggtgttgtggctttcgatccccctggtagttgc
ttattggggctgccaccaggtgtcagagattctTCgtCaTccgtCTTGCTccTtCGGCGaGAaAAGAAtctCGAG
AAGAAtccctgaCGCTTCTTtGGCGAaGCACTgGGcgtcggttgccttTTgGTGGGaCTtTGaTCaGGgGTtCGC
ATTATaATtataGGCGAagGtgtaGTtCtatTGGAgCTtAgGCTGCCGTTtCgCGAgCGgctcacagaaattgaa
tcactgacagcaCTCAGaTCCTGgGAGTTtctctgcGGtttcggtggtaagggaggtaatctctgatctgaaact
ggggaaGGaGTtCgaGGtGGcaatGGcAGgGGCGGtGAGgctGGgGGcGTGGCtGGtGTCTGaGCagcgTTcACT
TTgATCCTGGgaGCtGGtGGATTtGTcAGcACCACCAgtTCgtCaTCATCtAGCTGaCcaAAcGGATTGGTgggt
ggataaatgggggctgcttgtttgctttctttgggcaatcctatgtctAtgGGaTTaTTaaaggctatttGtAGg
CTcGTaTAtGTgGCtGTCTCaTCGAAgtTtTCaTCtAaATCCAtaGAgGCCTGGGCaCTGGCtgaaaccatttcc
ggttctttttcattttccggtagctctttcacgGCcGGATTCTCgAGgGTaTccctgcgagaaccattggccaaa
agaccgtgggcttccTCGTCcAacTGGTTCGTTATGGTCGTaTTGGCtGTCAaGCTGCTgACaTTgGTaAatgct
GTtTGGGCcGTGCTaTTCGAtAGgGattGcGTGTCCCCgTTCTCCACcGTCAGGCTaTCcGTTCtCTCgAACTCG
CTGCTCTTCATCCACTCggTgATtGTttCCACaTTGgacAGgGGtCGcGatTGcAGCTGCGGaTGCTGCAGaATC
TCCTCCATcGGCGTgGAcGTCTGgGTGCAGTCaTCGGCcAGtTGgGGCAaCAatTGCGGaACcTCCAGCTCtATT
TCCATaTCtGGTTCgTTaTCgTTaTCCGTGTACTCgGTgacagtgccaccatccatttcgtgcgattcacccctc
tgacgcattTGCAttTTCTTgACgGCtATcTCGAAtTCgTTgAGaGTtcCCGAaCTCTGttggtcaTCGGAtgaa
ACCGTGTTaTTaTccTCcTCcAGaTCcAtCGGtGGGCAcGAgTAtTTCGTGGCcGTcGTtTCGCTgTCtAgGGAA
AGgATCTGCTGGAAcACgTCCAgtTCCTGgcggCGtTTCAaCTTtCGCTGtAGCCGggCAAAgGTTActgTACCT
GGATTcGGgTAGTACTCGAAcgGCAGtgggGcaCTcGTCGCtccaTCcGAGGGTCtcactagtttcaGcTcCAcC
TGgaaggggggaaaaagtggagttagttctatttcattcgtgcaaaaaatttaaactcggaaaattaatgttttc
ggaagtacaagtattcgattaatggtacttagagcgcaaatgctattttcagtttattttacgttattaaatttg
ttttt
3) A miniexon in Mbs from splice sites AG.....GT as below
AGCTgAGtGATTCcACgGAaAGCTCACACttgACcAGtCTtTCCGAaAGCGAAGGT
4)A small ORF with wobble signature above pollux:  
ATGTTcActgtgccgtttcacCGGGAcACCATcCTGAC
caCcTCcGTCAGCGAtGCATCgGTgCTcAAcAAGAGtCGgGCCGTAtGTAgagattgggatccagtatccagtat
Attccgtatattcctattccgtattgcccgcatcgaaccactaacccctaaattgagcttgtgtaa
There is a perfect wobble signature in the EvoPrint.