I'm glad you found a solution that's working for you! Oddly, I wasn't able to reproduce the error:
library(magrittr)
library(kableExtra)
m.OutTab <- readr::read_csv(
"year,Population,GrowthRate,Population.1,GrowthRate.1
1990,265708,NA%,3304042,NA%
1995,312593,3.30%,3811074,2.90%
2000,351735,2.40%,4338801,2.60%
2005,395384,2.40%,4662534,1.40%
2010,443711,2.30%,5050332,1.60%
2015,489923,2.00%,5448055,1.50%
2016,497673,1.60%,5538180,1.70%"
)
ctyname <- "Starling City"
state <- "This State"
names_spaced <- c("Year", "Population", "Growth Rate", "Population", "Growth Rate")
tblHead <- c(" " = 1, ctyname = 2, state = 2)
names(tblHead) <- c(" ", ctyname, state)
OutTab <- m.OutTab %>%
knitr::kable(format = 'html', table.attr = 'class="myTable"',
caption = "Population Growth Rate",
row.names = FALSE,
align ='lrrrr',
col.names = names_spaced,
escape = FALSE) %>%
kable_styling(bootstrap_options = "condensed") %>%
column_spec(1, width = "0.4in") %>%
column_spec(2, width = "0.5in") %>%
column_spec(3, width = "0.5in") %>%
column_spec(4, width = "0.5in") %>%
column_spec(5, width = "0.5in") %>%
add_header_above(header = tblHead) %>%
add_footnote("This is the footnote for the table!")
Created on 2018-06-29 by the reprex package (v0.2.0).

> sessioninfo::session_info()
─ Session info ──────────────────────
setting value
version R version 3.5.0 (2018-04-23)
os Ubuntu 16.04.4 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate C.UTF-8
tz Etc/UTC
date 2018-06-29
─ Packages ──────────────────────────────────
package * version date source
backports 1.1.2 2017-12-13 RSPM (R 3.5.0)
clisymbols 1.2.0 2017-05-21 RSPM (R 3.5.0)
colorspace 1.3-2 2016-12-14 RSPM (R 3.5.0)
digest 0.6.15 2018-01-28 RSPM (R 3.5.0)
evaluate 0.10.1 2017-06-24 RSPM (R 3.5.0)
hms 0.4.2 2018-03-10 RSPM (R 3.5.0)
htmltools 0.3.6 2017-04-28 RSPM (R 3.5.0)
httr 1.3.1 2017-08-20 RSPM (R 3.5.0)
kableExtra * 0.9.0 2018-05-21 RSPM (R 3.5.0)
knitr 1.20 2018-02-20 RSPM (R 3.5.0)
magrittr * 1.5 2014-11-22 RSPM (R 3.5.0)
munsell 0.5.0 2018-06-12 RSPM (R 3.5.0)
pillar 1.2.3 2018-05-25 RSPM (R 3.5.0)
pkgconfig 2.0.1 2017-03-21 RSPM (R 3.5.0)
plyr 1.8.4 2016-06-08 RSPM (R 3.5.0)
R6 2.2.2 2017-06-17 RSPM (R 3.5.0)
Rcpp 0.12.17 2018-05-18 RSPM (R 3.5.0)
readr 1.1.1 2017-05-16 RSPM (R 3.5.0)
rlang 0.2.1 2018-05-30 RSPM (R 3.5.0)
rmarkdown 1.10 2018-06-11 RSPM (R 3.5.0)
rprojroot 1.3-2 2018-01-03 RSPM (R 3.5.0)
rstudioapi 0.7 2017-09-07 RSPM (R 3.5.0)
rvest 0.3.2 2016-06-17 RSPM (R 3.5.0)
scales 0.5.0 2017-08-24 RSPM (R 3.5.0)
sessioninfo 1.0.0 2017-06-21 RSPM (R 3.5.0)
stringi 1.2.3 2018-06-12 RSPM (R 3.5.0)
stringr 1.3.1 2018-05-10 RSPM (R 3.5.0)
tibble 1.4.2 2018-01-22 RSPM (R 3.5.0)
viridisLite 0.3.0 2018-02-01 RSPM (R 3.5.0)
withr 2.1.2 2018-03-15 RSPM (R 3.5.0)
xml2 1.2.0 2018-01-24 RSPM (R 3.5.0)
(I ran this in a new project on RStudio Cloud)